This experiment tests the consequence of a mutation at the FatB gene in the wound-response of Arabidopsis. The FatB mutant allele (fatb KD J. (Plant Cell 2003, Vol 15, 1020-1033)) was obtained from Dr. Katayonn Dehesh, of California, Davis, Davis, CA. This allele is in the Ws background.The growth conditions are as follows: 1. Seeds (between 14 and 16) are sown on in 100 x 100 x 15mm square Falcon Petri Dishes (Fisher Scientific, catalogue Seeds were arranged on the plates in a single horizontal line at the 1-cm mark the top of the plate.2. Each plate contains between 20 and 25-ml of sterile MS containing 0.1% (w/v) sucrose.3. Prior to sowing, seeds were sterilized by for 1 minute at room temperature with a 300-l solution of 50% (v/v) ethanol, solution was removed and replaced with a 300-l solution consisting of 1% (v/v) 20 (Fischer BioReagents, catalogue #BP33750), and 50% (v/v) bleach solution and incubated at room temperature for 10-minutes. The seeds were then washed three changes of 0.3-ml of sterile water.
Lipidomics studies on NIDDK / NIST human plasma samples
STUDY_TYPE
MS analysis on human plasma
STUDY_SUMMARY
The National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) in with the National Institute of Standards (NIST) recently produced a human standard reference material (SRM 1950) for metabolite analysis. The SRM was by obtaining plasma samples from 100 individuals between 40 and 50 years of whose ethnicity was representative of the US population and that included an number of men and women. The intent of the NIDDK/NIST project was to provide a material that would be publically available to researchers and that could be by the clinical chemistry community to identify plasma metabolites for purposes. Signature metabolites could then be further probed for their as disease biomarkers. The LIPID MAPS Consortium has undertaken the task to this SRM by systematically identifying and quantifying the lipid molecular in the six main categories of mammalian lipids. The quantitative levels of over different lipids present in this reference human plasma sample are presented
Timecourse on RAW 264.7 cells treated with Kdo2-Lipid A and compactin
STUDY_TYPE
Timecourse experiment
STUDY_SUMMARY
Lipidomics studies on macrophages - RAW 264.7 cells treated with Kdo2-Lipid A compactin. Experiments were conducted with RAW264.7 cells fed 10% fetal calf 8-timepoint study: Measurements were taken at 0, 0.5,1,2,4,8, 12, and 24hrs (i) compactin, (ii) Kdo2-Lipid A, (iii) compactin + Kdo2-Lipid A. and (iv)
In this study, seventeen white wines including Chardonnays, Viogniers, Pinot gris, Rieslings and Sauvignon blancs (which were part of a M.S. study in the Viticulture & Enology Department on white wine mouthfeel properties), were analyzed by GC-TOF. Additionally, chemical data obtained will be mined with the sensory data collected to further investigate the chemical basis for mouthfeel properties in wine.
INSTITUTE
University of California, Davis
DEPARTMENT
Davis Genome Center
LABORATORY
Fiehn
LAST_NAME
Kind
FIRST_NAME
Tobias
ADDRESS
451 E. Health Sci. Drive, Davis, California 95616, USA
Bacterial leaf blight (BLB), caused by Xanthomonas oryzae pv. oryzae (Xoo), rise to devastating crop losses in rice. Disease resistant rice cultivars are most economical way to combat the disease. The TP309 cultivar is susceptible to by Xoo strain PXO99. A transgenic variety, TP309_Xa21, expresses the pattern receptor Xa21, and is resistant. PXO99?raxST, a strain lacking the raxST gene, able to overcome Xa21-mediated immunity. We used a single extraction solvent to comprehensive metabolomics and transcriptomics profiling under sample limited and analyze the molecular responses of two rice lines challenged with either or PXO99?raxST. LCTOF raw data file filtering resulted in better within group of replicate samples for statistical analyses. Accurate mass match compound with molecular formula generation (MFG) ranking of 355 masses was achieved with METLIN database. GCTOF analysis yielded an additional 441 compounds after database processing, of which 154 were structurally identified by retention library matching. Multivariate statistics revealed that the susceptible and genotypes possess distinct profiles. Although few mRNA and metabolite were detected in PXO99 challenged TP309 compared to mock, many differential occurred in the Xa21-mediated response to PXO99 and PXO99?raxST. Acetophenone, fatty acids, alkaloids, glutathione, carbohydrate and lipid biosynthetic were affected. Significant transcriptional induction of several pathogenesis genes in Xa21 challenged strains, as well as differential changes to GAD, PAL, and Glutathione-S-transferase transcripts indicated limited correlation with changes under single time point global profiling conditions.
INSTITUTE
University of California, Davis
DEPARTMENT
Davis Genome Center
LABORATORY
Fiehn
LAST_NAME
Kind
FIRST_NAME
Tobias
ADDRESS
451 E. Health Sci. Drive, Davis, California 95616, USA
This experiment tests the effect of individual mutations on the metabolome of The standardized growth conditions are as follows: 1. Seeds (between 14 and 16) sown on media in 100 x 100 x 15mm square Falcon Petri Dishes (Fisher catalogue #08-757-11A). Seeds were arranged on the plates in a single line at the 1-cm mark from the top of the plate. 2. Each plate contains between and 25-ml of sterile MS media containing 0.1% (w/v) sucrose. 3. Prior to seeds were sterilized by treating for 1-minute at room temperature with a 300-l of 50% (v/v) ethanol, this solution was removed and replaced with a 300-l consisting of 1% (v/v) Tween 20 (Fischer BioReagents, catalogue #BP33750), and (v/v) bleach solution (Clorox), and incubated at room temperature for The seeds were then washed with three changes of 0.3-ml of sterile water. 4. sowing with seeds, the plates were wrapped with Micropore tape (3M Health Care, #1530-0), and then stored horizontally for 4-days at 4 °C, with of 1 mol/m2. 5. On the 5th day, plates were moved to the growth room, and held a vertical position in Plexi-glass holders for 17-days this growth room is labeled in Table I. 6. On 18th day Petri plates were opened and the aerial of these plants were harvested immediately upon plate opening. 7. Upon plant material was quenched by immersion in liquid nitrogen and stored at 70
INSTITUTE
University of California, Davis
DEPARTMENT
Davis Genome Center
LABORATORY
Fiehn
LAST_NAME
Kind
FIRST_NAME
Tobias
ADDRESS
451 E. Health Sci. Drive, Davis, California 95616, USA
To determine the basis of running capacity and health differences in outbread N/NIH rats selected for high capacity (HCR) and low capacity (LCR) running (a for VO2max) (see:Science. 2005 Jan 21;307(5708):418-20). Plasma collected at 12 of age in generation 28 rats after ad lib feeding or 40% caloric restriction at week 8 of age. All animals fasted 4 hours prior to collection between 5-8
Metabolomics Analysis of Thermally Challenged Mayfly Larvae (GCMS analysis)
STUDY_TYPE
Metabolomic analysis of mayflies
STUDY_SUMMARY
The purpose of this study was to examine the metabolic profiles of mayfly triangulifer) larvae subjected to thermal challenge. This species is unusual in of its ease of culture, and its suitability as a laboratory test organism. Our here was to examine how an environmentally realistic thermal challenge affects physiology of this organism. In this study, we obtained several types of insect and we were able to show that GC-MS Metabolomics could be used to distinguish the different types of larvae.
Plasma metabolomics: Comparison of non-diabetic controls with T1D patients
STUDY_TYPE
Drug effect study
STUDY_SUMMARY
Non-diabetic controls whose metabolites were compared to T1D patients with and insulin. Seven C-peptide?negative T1D subjects were studied on two occasions: during insulin treatment and the other following withdrawal of insulin for 8 h compared with matched healthy ND participants
Identification of altered metabolic pathways in Alzheimer's disease, mild impairment and cognitively normals using Metabolomics (plasma)
STUDY_TYPE
1
STUDY_SUMMARY
Criteria for the diagnosis of amnestic MCI included: (i) memory complaint by the patient and collateral source; (ii) impairment in 1 or more of the 4 domains (memory, executive functioning/attention, visuospatial, or language); essentially normal functional activities of daily living; and (iv) absence of In general, the amnestic MCI determination is made when the memory measures 1.0â??1.5 SD below the means for age and education appropriate individuals our community; however, rigid cutoffs on psychometric scores were not used to the diagnosis of amnestic MCI which was made on clinical grounds. The diagnosis dementia was made using DSM-IV criteria, and the diagnosis of AD was made using criteria. Subjects were considered to be CN if they performed within the range and did not meet criteria for MCI or dementia.
Identification of altered metabolic pathways in Alzheimer's disease, mild impairment and cognitively normals using Metabolomics (CSF)
STUDY_TYPE
MS
STUDY_SUMMARY
Criteria for the diagnosis of amnestic MCI included: (i) memory complaint by the patient and collateral source; (ii) impairment in 1 or more of the 4 domains (memory, executive functioning/attention, visuospatial, or language); essentially normal functional activities of daily living; and (iv) absence of In general, the amnestic MCI determination is made when the memory measures 1.0?1.5 SD below the means for age and education appropriate individuals in community; however, rigid cutoffs on psychometric scores were not used to the diagnosis of amnestic MCI which was made on clinical grounds. The diagnosis dementia was made using DSM-IV criteria, and the diagnosis of AD was made using criteria. Subjects were considered to be CN if they performed within the range and did not meet criteria for MCI or dementia.
Metabolomic & lipidomic profiles in response to exogenous insulin & GLP-1 during prolonged fasting (GCMS)
STUDY_TYPE
Timecourse
STUDY_SUMMARY
This application requests funding to access state-of-the-art metabolomics and platforms at the NIH West Coast Metabolomics Center to analyze plasma samples recent insulin and glucagon-like peptide-1 (GLP-1) infusion experiments in prolong-fasted elephant seals. This suite of studies was designed to better the mechanisms contributing to the onset of an insulin resistantlike condition by prolonged food deprivation/starvation in mammals. Because elephant seals evolved robust physiological mechanisms that have allowed them to naturally such protracted bouts of fasting, they provide an ideal model to address our hypothesis that increased lipid utilization late in the fast contributes to resistance in elephant seals. Insulin resistance is a common consequence of in mammals and, while the mechanisms by which it manifests are still unclear, a shift favoring increased mobilization and utilization of lipids during food deprivation may be a principal causative factor. Insulin resistance has a connotation due to its association with obesity and diabetes among humans, but has been suggested to be an adaptive response to food deprivation.
INSTITUTE
University of California, Davis
DEPARTMENT
GBSF
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
451 Health Sci Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
1-530-752-8258
NUM_GROUPS
5
TOTAL_SUBJECTS
117
STUDY_COMMENTS
5 general classes are designed in the experiment:#1 - A=No GLP1/ Late GTT#2 - (Low Dose)#3 - C=GLP1 (High Dose)#4 - IL- Early Fasting Insulin Infusion#5 - Late Fasting Insulin InfusionEach of the 5 classes has 6 timepoints (5x6):T1 - minT2 - 10 minT3 - 30 minT4 - 60 minT5 - 120 minEach timepoint had 5 animals (5 x 5 classes x 6 timepoints = 150 totalBecause certain animals and timepoints to be excluded 108 measurments remain.The experiment also contains 9 technical of pooled samples (pool)The total sample number is 108 (biological) + 9 pooled = 117
Metabolic Microenvironments in Normal Breast and Breast Cancer (MS analysis)
STUDY_TYPE
Metabolomic analysis of normal breast tissue
STUDY_SUMMARY
The purpose of this study was to understand the metabolomic changes in a breast microenvironment at various stages of cancer development and progression (i.e. breast, DCIS, and invasive cancer). The goal of this metabolomics pilot and study was to apply a broad spectrum GC-MS metabolomics method to determine changes in normal tissue of women with cancer correlate with progression and or subtype of the disease.
Combined Metabolomics and Lipidomics of Type 1 Diabetes (GCMS)
STUDY_TYPE
biomarker study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project granted to Bell (University of Chicago) and collaborator Manami Hara uses a multi-omics to investigate the metabolome (primary metabolites), lipidome (complex lipids) signaling lipids (oxylipins) in the plasma of Non-obese Diabetic (NOD) mice progressed to Type 1 Diabetes Mellitus (T1D) and those that did not. NOD Mice were assessed as diabetic or non-diabetic based on their fasting (4hr) blood levels at sacrifice, which defined 30 hyperglycemic (glucose = 250 mg/dL) and normoglycemic animals. The primary objective of this study was to identify biomarkers associated with beta-cell destruction/survival and T1D progression.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
Metabolite changes associated with methionine stress sensitivity of cancer (GC MS analysis)
STUDY_TYPE
timecourse study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project granted to Kaiser (UC Irvine), aims to achieve understanding of a unique metabolic of cancer cells to explore development of novel unconventional therapeutic that exploit dependence of cancer cells on methyl-donor abundance. The past few have highlighted the role of altered metabolism in cancer. While mechanistic into changed metabolism in cancer is very limited, the importance of the pathway surrounding homocysteine and methionine for cancer cell proliferation been known for over 30 years.These findings, generally summarized as or methionine stress sensitivity, describe the phenomenon that most cancer cannot proliferate in growth medium where the amino acid methionine is replaced its direct metabolic precursor homocysteine. Importantly, non-tumorigenic cells unaffected by replacing methionine with homocysteine in the growth medium. For past years we have been studying methionine dependence of breast and prostate and demonstrated that methionine-dependence is caused by insufficient flux this pathway to sustain synthesis of the downstream metabolite and the methyl-donor S-adenosylmethionine (SAM).We have isolated rare cell clones from breast cancer cells (referred to as MB468RES) that are no longer methionine and proliferate in homocysteine medium. Interestingly, MB468RES have lost their for anchorage independent growth, a hallmark of cancer. The MB468 and MB468RES line pair confirms other observations showing that methionine dependence is linked to tumorigenicity. Importantly, this cell line pair is an ideal model to metabolite signatures linked to cancer cell methionine dependence. We propose characterize the metabolic changes triggered by the shift from normal growth to homocysteine medium in MB468 breast cancer cells and the methionine stress MB468RES derivatives. In addition we have developed cancer cell lines with shRNAs targeting methionine adenosyltransferase (MAT), the enzyme catalyzing of SAM from methionine and ATP. Inducible knockdown of MAT allows us to reduce SAM synthesis. Our previous results suggest that SAM limitation is the trigger for cancer cell methionine dependence. Thus metabolite profiling using MAT knockdown system will provide an independent dataset that together with profiles from the MB468 and MB468RES cell line pair will define critical profiles related to cancer cell methionine dependence. In the current untargeted analysis of primary metabolites and complex lipids, coupled with analysis of methionine pathway intermediates (folate and respective s-adenosylmethoinine, s-adenosylhomocysteine, choline, betaine) and metabolic will be conducted on MB468, MB468RES and MB468shRNA following the switch from containing media to homocysteine containing media over the course of 0, 2, 4, 12, 24 and 48 hours. The primary objectives were to 1) characterize the response to methionine stress and SAM limitation and 2) correlate the metabolic with cancer cell proliferation arrest and death.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
Biomarkers for Depression in Human Plasma in a Population Sample
STUDY_TYPE
biomarker study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project was granted Roel Ophoff (UC Los Angeles ) and Steve Horwath (UC Los Angeles ) . Major disorder (MDD) is one of the most debilitating disorders in the United States a 12-month prevalence of 6.7% in the adult population. The disorder affects of Americans daily and is a major health concern with enormous economic cost society at large. Criteria for MDD diagnosis and treatment are based on various and symptoms not always fitting into strict diagnostic categories such as Despite various known risk factors (such as family history, age, and gender), markers supporting diagnosis or prediction of MDD are unavailable. We have cerebrospinal fluid (CSF) and peripheral blood of more than 600 subjects from general population. For each of the participants we also obtained biometric as well as behavioral trait measures. One of the measures is the Beck Inventory (BDI), a well-established questionnaire for measuring severity of Based on the BDI, roughly 5% of participants suffer from severe depressive while most of these subjects are not under treatment or receiving any for depression In the current investigation, untargeted analysis of primary was conducted on age and gender matched human cerebrospinal fluid (CSF) and from subjects suffering with MDD ( n=50) and control subjects (n=50). were diagnosed as having MDD based on the Beck Depression Inventory.The primary of this study were to 1) identify metabolites which discriminate between with and without depression symptoms in the CSF and plasma and 2) how changes between CSF and plasma.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
Metabolic Profiling of Visceral and Subcutaneous Adipose Tissue from Colorectal Patients: GC-TOF MS analyis of serum samples
STUDY_TYPE
biomarker study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project was granted Johanna Lampe (Fred Hutchinson Cancer Research Center at Univ. of Washington, In the current investigation, unbiased profiling of the metabolome and lipidome adipose tissue samples (visceral(VAT) and subcutaenous (SAT)) and serum of 50 patients, including stages I-IV, from the Fred Hutchinson Cancer Center and the German Cancer Research Center (Heidelberg, Germany) was conducted. The and metabolome of adipose tissue (VAT/SAT) and serum were analyzed using UPLC-QTOFMS analysis and GC-TOFMS analyses, respectively. The primary of this project were to 1) compare the metabolome and lipidome SAT adipose tissue of n=50 Colorectal Cancer Cell (CRC) patients, 2) the associations between the lipidome and metabolome in adipose tissue and serum of n=50 CRC patients and 3) test the associations between the of VAT and serum with the tumor stage of CRC patients.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
Combined Metabolomics and Lipidomics of Type 1 Diabetes (QTOF)
STUDY_TYPE
biomarker study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project granted to Bell (University of Chicago) and collaborator Manami Hara uses a multi-omics to investigate the metabolome (primary metabolites), lipidome (complex lipids) signaling lipids (oxylipins) in the plasma of Non-obese Diabetic (NOD) mice progressed to Type 1 Diabetes Mellitus (T1D) and those that did not. NOD Mice were assessed as diabetic or non-diabetic based on their fasting (4hr) blood levels at sacrifice, which defined 30 hyperglycemic (glucose = 250 mg/dL) and normoglycemic animals. The primary objective of this study was to identify biomarkers associated with beta-cell destruction/survival and T1D progression.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
Metabolite changes associated with methionine stress sensitivity of cancer (CSH MS analysis)
STUDY_TYPE
timecourse study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project granted to Peter Kaiser (UC Irvine), aims to achieve understanding of a unique metabolic dependence of cancer cells to explore development of novel unconventional therapeutic strategies that exploit dependence of cancer cells on methyl-donor abundance. The past few years have highlighted the role of altered metabolism in cancer. While mechanistic insight into changed metabolism in cancer is very limited, the importance of the metabolic pathway surrounding homocysteine and methionine for cancer cell proliferation has been known for over 30 years. These findings, generally summarized as methionine-dependence or methionine stress sensitivity, describe the phenomenon that most cancer cells cannot proliferate in growth medium where the amino acid methionine is replaced with its direct metabolic precursor homocysteine. Importantly, non-tumorigenic cells are unaffected by replacing methionine with homocysteine in the growth medium. For the past years we have been studying methionine dependence of breast and prostate cancer and demonstrated that methionine-dependence is caused by insufficient flux through this pathway to sustain synthesis of the downstream metabolite and the principal methyl-donor S-adenosylmethionine (SAM). We have isolated rare cell clones from MDA-MB468 breast cancer cells (referred to as MB468RES) that are no longer methionine dependent and proliferate in homocysteine medium. Interestingly, MB468RES have lost their ability for anchorage independent growth, a hallmark of cancer. The MB468 and MB468RES cell line pair confirms other observations showing that methionine dependence is tightly linked to tumorigenicity. Importantly, this cell line pair is an ideal model to identify metabolite signatures linked to cancer cell methionine dependence. We propose to characterize the metabolic changes triggered by the shift from normal growth medium to homocysteine medium in MB468 breast cancer cells and the methionine stress insensitive MB468RES derivatives. In addition we have developed cancer cell lines with inducible shRNAs targeting methionine adenosyltransferase (MAT), the enzyme catalyzing synthesis of SAM from methionine and ATP. Inducible knockdown of MAT allows us to specifically reduce SAM synthesis. Our previous results suggest that SAM limitation is the critical trigger for cancer cell methionine dependence. Thus metabolite profiling using the MAT knockdown system will provide an independent dataset that together with metabolite profiles from the MB468 and MB468RES cell line pair will define critical metabolic profiles related to cancer cell methionine dependence. In the current investigation, untargeted analysis of primary metabolites and complex lipids, coupled with quantitative analysis of methionine pathway intermediates (folate and respective derivatives, s-adenosylmethoinine, s-adenosylhomocysteine, choline, betaine) and metabolic flux will be conducted on MB468, MB468RES and MB468shRNA following the switch from methionine containing media to homocysteine containing media over the course of 0, 2, 4, 8, 12, 24 and 48 hours. The primary objectives were to 1) characterize the metabolic response to methionine stress and SAM limitation and 2) correlate the metabolic signatures with cancer cell proliferation arrest and death.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
Metabolic Profiling of Visceral and Subcutaneous Adipose Tissue from Colorectal Patients: UHPLC-QTOF MS analyis of subcutaneous and visceral adipose tissue
STUDY_TYPE
biomarker study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project was granted Johanna Lampe (Fred Hutchinson Cancer Research Center at Univ. of Washington, In the current investigation, unbiased profiling of the metabolome and lipidome adipose tissue samples (visceral(VAT) and subcutaenous (SAT)) and serum of 50 patients, including stages I-IV, from the Fred Hutchinson Cancer Center and the German Cancer Research Center (Heidelberg, Germany) was conducted. The and metabolome of adipose tissue (VAT/SAT) and serum were analyzed using UPLC-QTOFMS analysis and GC-TOFMS analyses, respectively. The primary of this project were to 1) compare the metabolome and lipidome SAT adipose tissue of n=50 Colorectal Cancer Cell (CRC) patients, 2) the associations between the lipidome and metabolome in adipose tissue and serum of n=50 CRC patients and 3) test the associations between the of VAT and serum with the tumor stage of CRC patients.Â
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
NUM_GROUPS
2
TOTAL_SUBJECTS
59
STUDY_COMMENTS
Lipidomics profiles for studyThis is the SAT and VAT part of the studyLabel-ID conserved for all parts of the study---The samples had to be diluted for mode measurements (therefore 2 dilutions are measured for the same sample). are then combined and scaling factor is used for final results.
A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Infection
STUDY_TYPE
Timecourse of Infection
STUDY_SUMMARY
The potential for commensal microorganisms indigenous to a host (the or microbiota) to alter infection outcome by influencing host-pathogen is largely unknown. We used a multi-omics systems approach, proteomics, metabolomics, glycomics, and metagenomics, to explore the molecular between the murine host, the pathogen Salmonella enterica serovar Typhimurium Typhimurium), and commensal gut microorganisms during intestinal infection with Typhimurium. We find proteomic evidence that S. Typhimurium thrives within the 129/SvJ mouse gut without antibiotic pre-treatment, inducing inflammation and the intestinal microbiome (e.g., suppressing Bacteroidetes and Firmicutes while growth of Salmonella and Enterococcus). Alteration of the host microbiome structure was highly correlated with gut environmental changes, including the of metabolites normally consumed by commensal microbiota. Finally, the less phase of S. Typhimuriums lifecycle was investigated, and both proteomic and evidence suggests S. Typhimurium may take advantage of increased fucose to metabolize fucose while growing in the gut. The application of multiple measurements to Salmonella-induced intestinal inflammation provides insights complex molecular strategies employed during pathogenesis between host, and the microbiome.
Model-driven multi-omic data analysis elucidates metabolic immunomodulators of activation
STUDY_TYPE
growth condition, timecourse
STUDY_SUMMARY
Macrophages are central players in immune response, manifesting divergent to control inflammation and innate immunity through release of cytokines and signaling factors. Recently, the focus on metabolism has been reemphasized as signaling and regulatory pathways of human pathophysiology, ranging from cancer aging, often converge on metabolic responses. Here, we used genome-scale and multi-omics (transcriptomics, proteomics, and metabolomics) analysis to metabolic features that are critical for macrophage activation. A genome-scale network for the RAW 264.7 cell line was constructed to determine metabolic of activation. Metabolites well-known to be associated with immunoactivation and arginine) and immunosuppression (tryptophan and vitamin D3) were among the critical effectors. Intracellular metabolic mechanisms were assessed, a suppressive role for de-novo nucleotide synthesis. Finally, underlying mechanisms of macrophage activation were identified by analyzing multi-omic obtained from LPS-stimulated RAW cells in the context of our flux-based This study demonstrates that the role of metabolism in regulating activation be greater than previously anticipated and elucidates underlying connections activation and metabolic effectors. This submission corresponds to the data from this study.
Salmonella Modulates Metabolism during Growth under Conditions that Induce of Virulence Genes
STUDY_TYPE
growth conditions, timecourse
STUDY_SUMMARY
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a facultative that uses complex mechanisms to invade and proliferate within mammalian host To investigate possible contributions of metabolic processes to virulence in S. grown under conditions known to induce expression of virulence genes, we used a systems biology approach coupled with genome scale modeling. First, we distinct metabolite profiles associated with bacteria grown in either rich or media and report the most comprehensive coverage of the S. Typhimurium to date. Second, we applied an omics-informed genome scale modeling analysis of functional consequences of adaptive alterations in S. Typhimurium metabolism growth under our conditions. Modeling efforts highlighted a decreased cellular to both produce and utilize intracellular amino acids during stationary phase in virulence conditions, despite significant abundance increases for these as observed by our metabolomics measurements. Furthermore, analyses of omics in the context of the metabolic model indicated rewiring of the metabolic to support pathways associated with virulence. For example, cellular of polyamines were perturbed, as well as the predicted capacity for secretion uptake.
Quantitative Metabolomics by 1H-NMR and LC-MS/MS Confirms Altered Metabolic in Diabetes
STUDY_TYPE
Pre- and Post- insulin study with matched controls
STUDY_SUMMARY
We obtained plasma samples from 7 c-peptide negative type 1 diabetic (T1D) and 7 non-diabetic controls (Con) that were matched for age (T1D = yrs, Con = 30.2±3.4 yrs), body mass (T1D = 80.2±4.7kg, Con = 81.9±7.4 kg) BMI (T1D = 26.5±1.2 kg/m2, Con = 25.2±1.3 kg/m2). Type 1 diabetic people were while treated with insulin and also after 8 hours of insulin deprivation
Metabolomics Analysis of Frontal Fibrosing Alopecia
STUDY_TYPE
Unaffected and Affected patient scalp biopsies
STUDY_SUMMARY
Scarring alopecia consists of a collection of disorders characterized by of hair follicles, replacement with fibrous scar tissue, and irreversible hair Alopecia affects men and women worldwide and can be a significant source of stress and depression for affected individuals. The purpose of this study was explore metabolic profiles in scalp tissue samples from normal control subjects and in matched samples obtained from affected (n=12) and unaffected (n=12) of the scalp in patients with lymphocytic Frontal Fibrosing Alopecia (FFA). fibrosing alopecia results from destruction of hair follicles by an lymphocytic infiltrate that is localized around the upper portion of the hair
INSTITUTE
Case Western Reserve University
DEPARTMENT
Dermatology
LABORATORY
Karnik Lab
LAST_NAME
Karnik
FIRST_NAME
Pratima
ADDRESS
-
EMAIL
psk11@case.edu
PHONE
216-368-0209
NUM_GROUPS
3 groups-Paired unaffected and affected (n=12),Normals(n=6)
TOTAL_SUBJECTS
Patients (N=12), Normals (N=6)
STUDY_COMMENTS
Affected scalp biopsies were obtained from frontal scalp, Unaffected from scalp. Normal scalp biopsies were obtained from the occipital scalp.
Metabolomic and lipidomic profiles in response to exogenous insulin and GLP-1 during prolonged fasting
STUDY_TYPE
Timecourse
STUDY_SUMMARY
Seventeen northern elephant seal pups constituting four different cohorts at Nuevo State Reserve were studied at two post-weaning periods: early (1-2 wk weaning; n=5) and late (6-7 weeks post weaning; n=12). Study #1: Prior to each protocol, plasma U/kg). Following the infusion, blood samples were collected at determine the effects of prolonged fasting on peripheral insulin activity and samples were collected. Ten fasting seal pups (n=5 early, n=5 late) were (i.v.) with a mass-specific dose of insulin (0.065 U/kg). Following the blood samples were collected at 10, 30, 60, 90, and 120 minutes. Study #2: late-fasted seal pups were administered either a low (LDG; 10 pmol/kg; n=3) or (HDG; 100 pmol/kg; n=4) dose of GLP-1 immediately following a glucose bolus g/kg) (i.v.) infused within 2 mins. the infusions, blood samples were collected 10, 30, 60, 90, 120, and 150 minutes.
SIRM Analysis of human P493 cells under hypoxia in [U-13C/15N] labeled medium (Positive ion mode FTMS)
STUDY_TYPE
tracer
STUDY_SUMMARY
SIRM Analysis of MYC inducible P493 cells under normoxia and hypoxia in labeled Glutamine medium
INSTITUTE
University of Kentucky
DEPARTMENT
Toxicology
LAST_NAME
Fan
FIRST_NAME
Teresa
ADDRESS
-
EMAIL
twmfan@gmail.com
PHONE
-
NUM_GROUPS
4
TOTAL_SUBJECTS
8
STUDY_COMMENTS
For protocols and additional information, see Le, A., Lane, A.N., Hamaker, M., S., Barbi, J., Tsukamoto, T., Rojas, C.J., Slusher, B.S., Zhang, H., Zimmerman. Liebler, D.C., Slebos, R.J.C., Lorkiewicz, P.K., Higashi, R.M., Fan, T.W-M., Dang, C.V. Cell Metabolism 15, 110 (2012). 13C/15N Gln was used as the tracer this study, even though the analysis did not explicity look for 15N
Targeted lipids were quantified and compared to the quantities of other labs the nation. Comparisons were between pooled serum from humans who have consumed seed for the past month, pooled serums from humans who have consumed fish oil the last month, and pooled serum from humans who have not consumed either flax or fish oil for the past month. Pooled samples were prepared in triplicate.
INSTITUTE
University of Florida
DEPARTMENT
College of Medicine, Department of Pathology, Immunology, and Laboratory
Aliquots of Jurkat T-lymphocyte cells were washed with 5 different rinsing (0.3% amm. formate, 0.3% amm. acetate, 0.9% NaCl, 1 M PBS, 100 mM PBS) and ran triplicate to monitor the effect of ion suppression on the electrospray signal.
Metabolic analysis of Normal Mouse Lung Fiboblasts with/without TGFbeta treatment (Part 1)
STUDY_TYPE
Glycolysis/TCA/Nucleotide analysis (tissue/cells)
STUDY_SUMMARY
This study is a part of series performed for the same researcher through pilot/feasibility grant program, so the publication is relevant reference for other studies, see the project for this study. This specific experiment is a small pilot study to establish method performance, it includes four biological replicas of identical cell cultures after the identical treatment and a single tissue sample.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Jurkat parental cells (JP6) or cells stably expressing the pCDNA Noxa vector (N5) cells were cultured to confluence and counted. 20E6 cells in triplicate were resuspended in glucose free or glutamine free medium for 2 hours. Cells were then pelleted and resuspended in 13C-1,2 Glucose (10mM) or 13C-U-glutamine (4mM) for 24 hours. Cells were pelleted and spent medium was collected. Cell pellets were washed 1X with ice cold PBS and cell pellets were resuspended in 400ul -20 methanol. Cells and media were snap frozen in liquid nitrogen and stored at -80.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
High Insulin Combined With Essential Amino Acids Stimulates Skeletal Muscle Protein Synthesis While Decreasing Insulin Sensitivity in Healthy Humans
STUDY_TYPE
High and low insulin with and without essential amino acids
STUDY_SUMMARY
Thirty participants were randomized to 3 groups of 10 each with each studied twice. Study groups comprised (1) low and high insulin, (2) low insulin and without EAAs, and (3) high insulin with and without EAAs.
Flies were fed a normal diet or high-sugar (30% sucrose) diet for 7 days. of flies fasted for 24h or sated were microdissected and immediately frozen in ice. The microdissection process from taking the fly out of the vial to the brain took less than a minute. Each brain microdissected piece contains 50K cells.We dissected 40 brains per condition (4 conditions total) and 4-5 replicates
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Human fecal bile acid profiles before and after fecal transplant
STUDY_TYPE
Understand the bile acid profiles from the feces of fecal microbiota transplant patients that successfully recover from recurrent C. difficile infection
STUDY_SUMMARY
Understand the bile acid profiles from the feces of fecal microbiota transplant patients that successfully recover from recurrent C. difficile infection
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
U13C-Glutamine and U13C-Glucose Flux Analysis (MFA SiHa B16F10)
STUDY_TYPE
SiHa_NT and SiHa_L are 2 experimental group, control and treatment incubated with U13Cglutamine before lysis for 2 hours. SiHa_WT and SiHa_F3 are different cell isogenic clones to incubated before lysis with U13C glucose for Similarly, B1610 and B16M4 are 2 cell lines incubated before lysis with U13C for 2hours
STUDY_SUMMARY
SiHa_NT and SiHa_L are 2 experimental group, control and treatment incubated with U13Cglutamine before lysis for 2 hours. SiHa_WT and SiHa_F3 are different cell isogenic clones to incubated before lysis with U13C glucose for Similarly, B1610 and B16M4 are 2 cell lines incubated before lysis with U13C for 2hours
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
This experiment was performed using the following cohorts: 1) healthy controls, patients with scleroderma at low risk for pulmonary hypertension, 3) pateints scleroderma at high risk for pulmonary hypertension. Whole blood was drawn into stop soilution (1:1 ratio) at rest and again at peak exercise for each subject.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolomic analysis of normal and diabetic mouse bone marrow under PBS or treatment
STUDY_TYPE
Untargeted Metabolomics
STUDY_SUMMARY
Wild type and diabetic (MKR) mice were treated daily with intraperitoneal of 50 microliters of PBS (control) or metformin (200 mg/kg body weight) for 14 Their bone marrow cells were collected and compared by untargeted metabolomics.
INSTITUTE
New York University
DEPARTMENT
College of Dentistry, Basic Science and Craniofacial Biology
LABORATORY
Xin Li Laboratory
LAST_NAME
Xin
FIRST_NAME
Li
ADDRESS
345 East 24th Street, Room 901D, New York, NY 10010
EMAIL
xl15@nyu.edu
PHONE
1-(212)992-7009
NUM_GROUPS
4
TOTAL_SUBJECTS
15 samples
STUDY_COMMENTS
each sample with 3 technical replicates in each mode
Effect of Insulin Sensitizer Therapy on Amino Acids and Their Metabolites
STUDY_TYPE
drug + time course
STUDY_SUMMARY
We previously reported the overall study design for the parent study [29]. The report primarily examines the effect of three months of insulin sensitizer on plasma concentrations of BCAA, AAA, and AA metabolites in overweight/obese with fasting hyperglycemia, defined as either impaired fasting glucose or diabetes [29]. Briefly, 25 drug naïve, Northern European American participants fasting blood glucose concentrations of 108?180 mg/dL were randomized to either 45 mg of pioglitazone per day plus 1 g of metformin twice per day (n = or placebo (n = 13) for 12 weeks. We chose metformin based on its proven effect hepatic insulin sensitivity and pioglitazone based on its effect on peripheral sensitivity. Current use of hypoglycemic medications excluded participants from present study.
In this experiment 2 day old baby mice were exposed to hyperoxia (75% O2) for 14 days. Control baby mice were housed in room air (normoxia). Plasma and lavage fluid (BALF) were harvested after 14 days of exposure (on Day of life
STUDY_SUMMARY
In this experiment 2 day old baby mice were exposed to hyperoxia (75% O2) for 14 days. Control baby mice were housed in room air (normoxia). Plasma and lavage fluid (BALF) were harvested after 14 days of exposure (on Day of life
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Comparative metabolomics study of WT and iButOH tolerant E. coli
STUDY_SUMMARY
This study aims to elucidate metabolic mechanisms of tolerance to isobutanol in coli. Two strains are utilized: WT parental strain EcHW24, and isobutanol strain 38-20-4 created via multiplex genome engineering. The metabolic response growth with isobutanol (0.7% w/v) and without (0% w/v) on NG50 minimal media be compared for each strain. 3 replicates for each strain/iButOH concentration been submitted, excpet for WT/0.7%; we have observed high growth phenotype for this combination, and have corresponding submitted 5x replicates. Strain contains mutations in the TCA cycle (gltA SNP) and amino acid metabolism indels in glnE, gltD, and tnaA), thus our hypothesis is that tolerance arises rewiring of TCA cycle and amino acid metabolism, possibly resulting in intracellular ratio of glutamine:glutamate
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
The experiment was done on 4/2/2014 and consists of 7 experimental conditions x replicates per condition = 14 samples. The experimental duplicates are numbered (i.e. 1 and 2, 3 and 4, etc.). All samples are primary mouse macrophages from bone marrow. 12 million cells were plated in each 10 cm tissue culture plate (Corning) and the following day the cells were stimulated with LPS, CL097 and/or Gardiquimod in 10 mls of 2% FBS 25 mM HEPES IMDM. After 60 minutes medium was aspirated and the cells were rapidly wahsed with 15 mls of 150 mM acetate and after aspiration liquid nitrogen was poured on top of the cells and to -80 C freezer. Sample pairs 7 - 8 and 9-10 were treated identically except the rinse was done with ammonium acetate (7 and 8) or distilled water (9 and to evaluate the effect of the rinse solution in the quality of the obtained
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
T cell metabolism during graft-versus-host disease (CAB 307)-PART I
STUDY_TYPE
Glycolysis/TCA/Nucleotide analysis (tissue/cells)
STUDY_SUMMARY
T cells were injected into mice to model graft-versus-host disease. On day 7 after bone marrow transplantation (BMT), cells were recovered and CD8 T cells were purified to > 90% purity over magnetic columns. Naïve T cells were used as control. Cells were then plated at 5x10^6 cells/ml onto plates coated with anti-CD3/CD28 antibodies in the presence of 300µM 13C-palmitate conjugated to BSA (in PBS). Cells were incubated at 37oC for 60min, after which time they were removed from the plates, counted, and an equal number (2.5x10^6) were placed into a 1.7 ml micro-centrifuge tubes and spun down. Cells were washed once with ammonium chloride, residual volume was removed by a second brief spin, cell pellets were flash frozen in liquid nitrogen and stored at -80oC until analysis. Several mice lines were used in this study.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
We recently reported superior right ventricle (RV) performance in response to acute afterload challenge in lambs with a model of congenital heart disease with chronic left-to-right cardiac shunts. Compared with control animals, shunt lambs demonstrated increased contractility because of an enhanced Anrep effect (the slow increase in contractility following myocyte stretch). This advantageous physiological response may reflect preservation of a fetal phenotype, since the RV of shunt lambs remains exposed to increased pressure postnatally. Nitric oxide (NO) production by NO synthase (NOS) is activated by myocyte stretch and is a necessary intermediary of the Anrep response. The purpose of this study was to test the hypothesis that NO signaling is increased in the RV of fetal lambs compared with controls and shunt lambs have persistence of this fetal pattern. An 8-mm graft was placed between the pulmonary artery and aorta in fetal lambs (shunt). NOS isoform expression, activity, and association with activating cofactors were determined in fetal tissue obtained during late-gestation and in 4-wk-old juvenile shunt and control lambs. We demonstrated increased RNA and protein expression of NOS isoforms and increased total NOS activity in the RV of both shunt and fetal lambs compared with control. We also found increased NOS activation and association with cofactors in shunt and fetal RV compared with control. These data demonstrate preserved fetal NOS phenotype and NO signaling in shunt RV, which may partially explain the mechanism underlying the adaptive response to increased afterload seen in the RV of shunt lambs. Research is published, core data not used but project description is relevant: http://ajpheart.physiology.org/content/309/1/H157.long
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
This experiment was performed in wild type vs. CD39 knockout (KO) mice that had infusions of either saline or apyrase over the course of 2 weeks. Whole blood obtained via intracardiac puncture, and was drawn into a syringe prefilled with anti-enzyme stop solution.
STUDY_SUMMARY
This experiment was performed in wild type vs. CD39 knockout (KO) mice that had infusions of either saline or apyrase over the course of 2 weeks. Whole blood obtained via intracardiac puncture, and was drawn into a syringe prefilled with anti-enzyme stop solution.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Patients between age of 6 weeks and 16 years of age who were undergoing small resection were selected, including those who were either receiving enteral preoperatively (control group), or those who were without enteral nutrition and TPN (TPN group). At the time of operation, 100-500 microliters of effluent from small bowel lumen was aspirated during the small bowel resection. The samples immediately frozen in liquid nitrogen and stored at -80deg. After five control five TPN samples were collected, all samples were submitted for amino acid to quantify the relative amounts of amino acids in the small bowel effluent each patient. We hypothesize that the TPN group will contain higher levels of amino acids present in TPN, such as leucine, phenylalanine, and valine.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Samples 4-34 are sera and feces from an experiment to determine the effects of on SCFA in Ang II-induced hypertension. Samples 35-59 are plasma samples fron experiment to determine the effects of ACE2 activator, DIZE on SCFA in pulmonary hypertension. Plasma samples were collected using heparin
STUDY_SUMMARY
Samples 4-34 are sera and feces from an experiment to determine the effects of on SCFA in Ang II-induced hypertension. Samples 35-59 are plasma samples fron experiment to determine the effects of ACE2 activator, DIZE on SCFA in pulmonary hypertension. Plasma samples were collected using heparin
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
This is a time restricted feeding study (see M Hatori, et al. Cell Metabolism 15(6), 848-860)
STUDY_SUMMARY
This is a time restricted feeding study (see M Hatori, et al. Cell Metabolism 15(6), 848-860). Briefly, there are four groups of mice: (1) NA mice are on a chow ad libitum diet; (2) FA mice are on a high fat ad libitum diet (i.e. Diet obesity); (3) FT mice are on a high fat time restricted diet (i.e. only eat for hours/day and fast for 16); and (4) CDKO mice which are cry knock out mice on a chow ad libitum diet. We have collected stool from these four groups while they in the light and in the dark. Our expectation is that their stool metabolites be different at different times of the day.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Lanthanide-mineral induced alteration of bile acid metabolism in a murine model steatohepatitis
STUDY_SUMMARY
120 mice (equal number of males and females) were randomized into 3 equal One group is on a HFWD alone, a second group is on HFWD supplemented with and calcium, and a third control group is supplemented with calcium alone. At termination (18 months) we will harvest hepatocytes and colonic enterocytes for of epithelial gene expression patterns. We will also harvest cecal contents and for microbial profiling by 16S rRNA pyrosequencing. For this small pilot we wish to add an untargeted metabolomic analysis component. We will harvest (right medial lobe with gall bladder), serum, and feces. We will assay liver/gall bladder samples (8 from the HFWD group and 8 from the supplemented group). Remaining liver samples and the serum and feces will be for future investigation. Liver is being targeted first since both and hepatocellular carcinoma were seen in our previous study in mice on HFWD Additionally, alterations of bile acid profiles and bile acid metabolism have associated with both steatohepatitis and hepatic cancers.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Understand the differences in Bile Acid composition between knockout and floxed at each intestinal segment. Also difference in metabolites between these two at each level of the intestine.
STUDY_SUMMARY
Understand the differences in Bile Acid composition between knockout and floxed at each intestinal segment. Also difference in metabolites between these two at each level of the intestine.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Murine gastrointestinal bile acid profiles before and after antibiotics
STUDY_SUMMARY
Mice were treated with cefoperazone for 10 days and then allowed 6 weeks to off of the antibiotic. Other antibiotic treatments included IP clindamycin the 6 week recovery, IP clindamycin alone, vancomycin alone, kanamycin alone metronidazole. Gut luminal contents of these mice were collected at the time of and included both ileal and cecal content. Paired samples will be used for both analysis and targeted bile acid analysis to define how gut bacteria alter bile profiles in the gut and in turn how this affects C. difficle spore germination outgrowth.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Tumor neurospheres were grown in culture until 90% confluent. To collect cells, were filtered through 0.45um nylon filters (Fischer Sci 099029) that were with methanol and ultrapure water using a microanalytical glass filter holder Sci 09753E). The cells were filtered through filtration apparatus, then washed 1mL of distilled water very quickly. Filter paper is taken immediatedly with and plunged cell side down into 6-well plate filled with liquid nitrogen placed dry ice. Plate is wrapped in aluminum foil and stored at -80C before the liquid evaporates. Samples are shipped on dry ice
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Wild type and AMPK KO bone marrow derived macrophage were stimulated with LPS for various time period and plates were frozen in liquid nitrogen after washing sodium acetate (200uM) solution and kept in deep freezer for further analysis.
STUDY_SUMMARY
Wild type and AMPK KO bone marrow derived macrophage were stimulated with LPS for various time period and plates were frozen in liquid nitrogen after washing sodium acetate (200uM) solution and kept in deep freezer for further analysis.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
T cell metabolism during graft-versus-host disease (CAB 307)-PART II
STUDY_SUMMARY
T cells were injected into mis-matched animals undergoing bone marrow On day 7 after BMT, cells were receovered and CD8 T cells were purified to > purity over magnetic column. Cells were washed once in PBS, then once in chloride, residual volume was removed and cell pellets were flash frozein in and stored at -80C
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Changes to bile acids in the murine gut after antibiotics
STUDY_SUMMARY
Changes to bile acids in the murine gut after antibiotics
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@umich.edu
PHONE
-
NUM_GROUPS
12
TOTAL_SUBJECTS
60
STUDY_COMMENTS
Samples were collected at the time of necropsy. Contents from the lumen of the tract of C57BL/6 mice were collected, flash frozen and stored in the -80C until for metabolomics assay. C57BL/6 mice treated with cefoperazone for 5 days with days of water (n=5) were harvested along with non-antibiotic treated mice Contents from the small intesine (duodenum, jejunum and ileum), the large (cecum, colon) and stool were collected for targeted bile acid analysis.
Role of Microbiome in Psoriatic Arthritis (SCFA in PsA)
STUDY_SUMMARY
To investigate associations of gut and skin microbiota diversity with psoriatic pathogenesis.Characterize the abundance and diversity of gut microbiota in with never-treated, new-onset psoriatic arthritis (PsA). Methods: 16s rRNA pyrosequencing was utilized to compare the community composition of microbiota in PsA patients, psoriasis patients and healthy, matched controls. from patients with PsA, psoriasis of the skin (Ps), new-onset rheumatoid (NORA) and healthy controls were assessed for the presence and levels of fecal immunoglobulin A (sIgA) and various proteins and pro-inflammatory cytokines
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Normal plasma cells,Low proliferation multiple myeloma and High proliferation myeloma cells
STUDY_TYPE
differential metabolomics
STUDY_SUMMARY
CD138 sorted bone marrow plasma cell were obtained from a normal patient, a myelow with slow proliferation and a multiple myelow with rapid proliferation.
Bile acid targeted metabolomics of the small intestine in malnourished and mice
STUDY_TYPE
Targeted metabolomics
STUDY_SUMMARY
A total of 8 samples from 6 week old, female C57BL/6 mice, treated for 3 weeks a malnourished diet or a control-fed isocaloric diet. Samples were taken from small intestinal fecal content at the terminus of the ileum for targeted bile analysis.
INSTITUTE
University of Victoria
DEPARTMENT
The Uvic Proteomics and Metabolomics Innovation Centre
LAST_NAME
Borchers
FIRST_NAME
Christoph
ADDRESS
#3101-4464 Markham St Victoria, BC Canada, V8Z 7X8
EMAIL
christoph@proteincentre.com
PHONE
-
NUM_GROUPS
2
TOTAL_SUBJECTS
8*
STUDY_COMMENTS
*One sample failed quality control in the malnourished group, thus was not in the study
Vitamin targeted metabolomics of the small intestine in malnourished and mice
STUDY_TYPE
Targeted metabolomics
STUDY_SUMMARY
A total of 8 samples from 6 week old, female C57BL/6 mice, treated for 3 weeks a malnourished diet or a control-fed isocaloric diet. Samples were taken from small intestinal fecal content at the terminus of the ileum for targeted of vitamin concentrations.
INSTITUTE
University of Victoria
DEPARTMENT
The Uvic Proteomics and Metabolomics Innovation Centre
LAST_NAME
Borchers
FIRST_NAME
Christoph
ADDRESS
#3101-4464 Markham St Victoria, BC Canada, V8Z 7X8
Concentrations of cocaine (5,3,2,1.5,1,0.75,0.5,0.25,0.125, 0.062, and 0.031 were spiked into whole human blood for MALDI-MS analysis. A 10 uL volume of mixture was allowed to dry on Whatman Grade 2 filter paper. A 1ppm Cocaine-d3 was used as an internal standard. Parameters of the MALDI system optimized, including laser energy, number of laser shots, and matrix. The standard was added on top of the dried blood spot sample. Wide isolation tandem was used to generate a calibration curve.
INSTITUTE
University of Florida
DEPARTMENT
Chemistry
LABORATORY
Chemistry Lab Building
LAST_NAME
Dhummakupt
FIRST_NAME
Elizabeth
ADDRESS
R3-226 Academic Research Building, Department of Biochemistry and Molecular PO Box 100245, Gainesville, FL 32610-0245
EMAIL
emuffly@ufl.edu
PHONE
352-392-0515
NUM_GROUPS
11
TOTAL_SUBJECTS
154
STUDY_COMMENTS
11 concentrations were run as 7 samples/concentration for 2 days
Analysis of Dried Blood Spots by Paper Spray Ionization - MS
STUDY_TYPE
Analysis of Dried Blood Spots by Paper Spray Ionization - MS
STUDY_SUMMARY
Concentrations of cocaine (6, 5,3,2,1.5,1,0.75,0.5,0.25,0.125, 0.062, and 0.031 were spiked into whole human blood for PS-MS analysis. A 10 uL volume of mixture was allowed to dry on Whatman Grade 2 filter paper. A 1ppm Cocaine-d3 was used as an internal standard. Parameters of the paper spray were optimized, including spray voltage, capillary temperature and solvent. The standard was added on top of the dried blood spot sample. Wide isolation tandem was used to generate a calibration curve.
INSTITUTE
University of Florida
DEPARTMENT
Chemistry
LABORATORY
Chemistry Lab Building
LAST_NAME
Dhummakupt
FIRST_NAME
Elizabeth
ADDRESS
R3-226 Academic Research Building, Department of Biochemistry and Molecular PO Box 100245, Gainesville, FL 32610-0245
EMAIL
emuffly@ufl.edu
PHONE
352-392-0515
NUM_GROUPS
11
TOTAL_SUBJECTS
154
STUDY_COMMENTS
11 concentrations were run as 7 samples/concentration for 2 days
Metabolomics Reveals that Aryl Hydrocarbon Receptor Activation by Environmental Induces Systemic Metabolic Dysfunction in Mice (Part II)
STUDY_TYPE
Time course
STUDY_SUMMARY
12 C57BL/6J male mice were acclimatized for 1 week and then divided into two and trained to eat dough pills. One group was control and the other was exposed TCDF through the dough pills. The mice were treated for 5 days at a dosage of TCDF for a final concentration of 5μg/kg body weight. Also looked at were mice and they were treated the same way as the C57BL/6J mice.
INSTITUTE
Pennsylvania State University
DEPARTMENT
Department of Veterinary and Biomedical Sciences
LAST_NAME
Patterson
FIRST_NAME
Andrew
ADDRESS
101 Life Sciences, University Park, State college, 16802
Adult (14 weeks old) Sprague-Dawley rats showing at least three consecutive periods (4 day) of estrous cycles were randomly assigned to four groups: 1: 2: nicotine (6 mg/kg), 3: OC and 4: nicotine (6 mg/kg) + OC. Rats were exposed these treatments for a month. At the end of treatments, hippocampus was immediately frozen in liquid nitrogen. We are sending one side of hippocampi to Center for Integrated Metabolomics for analysis at the University of Florida.
Cyclobutene- and cyclobutane-functionalized fatty acids as novel biochemical of structure and function in HepG2 cells
STUDY_TYPE
Lipid analysis novel C18 fatty acid anologues in complex lipids
STUDY_SUMMARY
Human hepatoma HepG2 cells (American Type Culture Collection; HB-8065) were in 75 ml tissue cell culture flasks in Eagle's minimal essential medium (EMEM) with 10% fetal bovine serum at 37°C in a humidified atmosphere with 5% CO2. treatment with fatty acids or analogues, the cells were seeded at a density of × 106 cells in a T25-cm2 flask for 24 h. Each FA or analogue was added to the medium as a fatty acid-bovine serum albumin (BSA) complex (2.5:1, FA:BSA) to the desired final concentration. The controls in these experiments were HepG2 with BSA alone. After 24 h treatment, the media was collected, cells were twice with PBS and cells were harvested for analysis. To each cell suspension to lipid extraction a standard mixture of 25 µg C15:0 PE, C17:0 PC and C71:1 was added as standards. Extraction of lipids was performed according to the method. For metabolomics analysis, the lipid extracts were resuspended in 2:1 (v/v).All analyses were carried out using an Agilent 1200 Series HPLC, ACE C8-300 column (2.1 x 100 mm) and linear gradient elution at a flow rate of 0.1 Mobile phase A and B consisted of 0.1% formic acid; 10 mM ammonium acetate in and 0.1% formic acid; 10 mM ammonium acetate in ACN/isopropanol (50/50; v/v), The injection volume was 4 µL. Separation of metabolites was achieved at the gradient: T=0 min: 30% B; T=1 min: 30% B; T=25 min: 100% B; T=45 min: 100% B; min: 30% B; and T=60 min: 30% B (re-equilibration). The HPLC system was coupled to a Bruker Soalrix 70 Hybrid FTMS instrument equipped with ionization source (ESI) (Bruker Daltonics). The system was controlled by HyStar software. MS data was collected with resolving power of 78,000 (at m/z 400) in or negative mode under following conditions: a capillary voltage of (+/-) 4,500 and an end plate offset of -500 V. The dry temperature was set at 180°C. Dry flow was maintained 4 L/min. Acquisition range was 244-1,800 m/z with 0.2 s ion time. LC-MS data was converted into mzXML format using CompassXport v. 3.0.6 processed by mzMine v.2.10 [25] or XCMS data analysis software. Data processing mass detection, chromatographic peak detection and deconvolution, isotopic grouping, normalization and peak alignment. Metabolite data were mean-centered unit-variance scaled to remove the offsets and adjust the importance of high low abundance metabolites to an equal level. Significantly altered metabolites defined by a fold change (FC) >2 and p<0.05. Principal component analysis (PCA) hierarchical clustering analysis (HCA) of signature metabolites altered in treated cells compared to control were performed in the Metaboanalyst web (www.metaboanalyst.ca).
INSTITUTE
University of Nebraska - Lincoln
DEPARTMENT
Biochemistry
LABORATORY
DiRusso Black FATTT Lab
LAST_NAME
DiRusso
FIRST_NAME
Concetta
ADDRESS
Department of Biochemistry, University of Nebraska-Lincoln, N241 Beadle Center Vine St.
EMAIL
cdirusso2@unl.edu
PHONE
402-472-6504 or 402-613-9293
NUM_GROUPS
8
TOTAL_SUBJECTS
24+24=48
STUDY_COMMENTS
8 groups in triplicate ran in both negative and positive mode
Whole unconditioned medium (Defined culture media, M199),Whole M1 medium,Whole medium
STUDY_TYPE
differential metabolomics
STUDY_SUMMARY
Media was flash frozen with N2 and stored at -80 C. Samples can be stored at C until use. ~1 ml aliquots. The following media has been provided to the core in biological triplicates.Complete (Whole) Media:1) Whole unconditioned (Defined culture media, M199)2) Whole M1 medium3) Whole M2 medium
Metabolomic-based investigation on the effects of antifungal agents in Candida
STUDY_TYPE
in vitro study/drug dosage
STUDY_SUMMARY
Our aim is to determine the metabolic effects of increasing doses of an agent on C. albicans metabolism (untargeted, steady state metabolomics). We culture in vitro Candida cells to the mid-logarithmic growth in liquid media at 37°C and then inoculate biological replicates (1ml) onto 22mm filters under vocuum filtration in sterile conditions. Subsequently, isolates be cultivated to midlogarithmic phase of growth on the same agar (RPMI-1640) to the antifungal agent has been added at a range of concentrations to achieve equivalent to 0 MIC (no drug), 0.0625 MIC, 0.125 MIC, 0.25 MIC, 0.5 MIC and 1.0 at 37°C. At mid-logarithmic phase of growth (12h) replicates will be quenched by immersion into a solvent mixture of 40% acetonitrile: 40% methanol: water precooled at -40°C. The resulting quenched isolate/solvent mixtrue will mechanically lysed by bead-beating with 0.1mm Zirconia beads in a tissue and then centrifuged to seperate out cell wall components. Supernatants will be and stored at -80°C until they will be sent to SECIM facility.
In this project we will investigate the feasibility of metabolomics and to the diversity of ?metabotypes? in the horse, towards discovery of markers and associated with obesity and insulin resistance in the equine model. The team of researchers assembled for this work have identified horses severely with Equine Metabolic syndrome, often characterized by obesity and These animals are all from the Arabian breed, to control for some genetic Horses are age, sex and farm of residence matched with a control animal possible. Carefully controlled collection protocols were utilized to ensure variability in sample age and quality. Blood plasma is submitted for both LC-MS analysis through the SECIM core facilities. This discovery-based approach begin to generate new targets for the development of novel therapeutic for the treatment and prevention of obesity, type-2 diabetes as well as related conditions in both humans and horses. Finally, as the first dataset of its kind the horse, we may also be able to highlight promising new biomarkers for diagnostic use.
Aliquots of Jurkat T-lymphocyte cells were extracted using the Folch or Matyash at different total volumes and run in triplicate to calculate the extraction for each method.
INSTITUTE
University of Florida
DEPARTMENT
Dept. of Chemistry/SECIM
LABORATORY
Biomedical Mass Spectrometry Lab
LAST_NAME
Ulmer
FIRST_NAME
Candice
ADDRESS
R3-226 Academic Research Building, Department of Biochemistry and Molecular PO Box 100245, Gainesville, FL 32610-0245
Determining the metabolic profile of wildtype and nos mutant Staphylococcus grown in media lacking glucose using targeted LC/MS
STUDY_TYPE
Single time point
STUDY_SUMMARY
Whole cells from wildtype, nos mutant, SrrAB mutant, SrrAB nos double mutant, complement strains will be isolated for targeted metabolite analysis. In supernatants (extracellular metabolites) will also be analyzed for their profile.
Measurement of free amino acid (AA) in response to MYC
STUDY_TYPE
treatment
STUDY_SUMMARY
The proposed study will provide us information how the different AAs are by MYC. MYC is known to cause increased levels of glutamin due to import and but we hypothesize that the overall pool of free AA in the cells is reduced, when cells are starved.
Impact of recurrent hypoglycemia on brain metabolite profile
STUDY_TYPE
Insulin treatment in diabetic rats
STUDY_SUMMARY
The goal of this study is to determine the effect of mild / moderate on brain metabolism. To achieve this goal insulin-treated diabetic rats will be to recurrent mild / moderate hypoglycemia.
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LAST_NAME
Dave
FIRST_NAME
Kunjan
ADDRESS
-
EMAIL
Kdave@med.miami.edu
PHONE
305-243-3590
NUM_GROUPS
2
TOTAL_SUBJECTS
40
STUDY_COMMENTS
Two groups (i) Insulin treated diabetic + Recurrent hypoglycemia, (ii) Insulin diabetic + Recurrent hypoglycemia (only insulin injection) + Glucose infusion maintain glucose to baseline levels.Total 40 samples. Description: Ten samples and 10 hypothalamus sample from ITD+RH group of rats.Similarly, Ten samples and 10 hypothalamus sample from ITD+RH+Glucose group of rats.
NIH WCMC Pilot & Feasibility Project: Metabolite changes associated with loss
STUDY_TYPE
Feeding study
STUDY_SUMMARY
Targeted metabolomic analyses of oxylipins, endocannabinoids, and ceramides performed on 18 mouse liver, adipose, hypothalamus, plasma, and muscle samples from mice euthanized at 18 weeks following consumption of three diet regimens induced lean, obese, and weight loss phenotypes. Samples were analyzed by using a Waters Acquity UPLC and detected on an API 4000 QTrap (AB Sciex, MA, USA) by multiple reaction monitoring (MRM) after negative mode electrospray
metabolic contriubtion of pSymA and pSymB megaplasmid/chromid for multipartite meliloti cultured in rich LBmc medium
STUDY_TYPE
megaplasmid deletion
STUDY_SUMMARY
We wished to evaluate the contribution of pSymA and pSymB towards the of various metabolites in a nutritionally complex environment and to examine S. meliloti influences its surrounding environment.
INSTITUTE
McMaster University
DEPARTMENT
Department of Biology
LAST_NAME
Finan
FIRST_NAME
Turlough
ADDRESS
Department of Biology, McMaster University, Hamilton, Canada L8S4K1
We analyzed metabolites in the brains of wild type mice and DJ-1 knockout mice. DJ-1 knockout mouse is a model of an inherited form of Parkinson's disease.
INSTITUTE
National Institute on Aging
DEPARTMENT
Laboratory of Neurogenetics
LABORATORY
Cell Biology and Gene Expression Section
LAST_NAME
Hauser
FIRST_NAME
David
ADDRESS
35 Lincoln Drive, BLDG 35, Room 1A-1012, Bethesda, MD 20892
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv1713
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in M. tuberculosis genome with whole-cell lysate and assaying changes in levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might
INSTITUTE
Weill Cornell Medical College
DEPARTMENT
Microbiology and Immunology
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 Avenue, New York, NY
EMAIL
kyr9001@med.cornell.edu
PHONE
-
NUM_GROUPS
3 replicates X 3 timepoints X with/without GTP
STUDY_COMMENTS
The timepoints in the datafiles refer the amount of time (in minutes) that each was incubated with lysate.The units for 'mzmed' are mass/charge.The units for are seconds (retention time).The units for all the other data columns in the are arbitrary; they are integrated peak counts.In this study, Rv1713 was with lysate with and without 1mM GTP added as a co-factor.
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv1016
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in M. tuberculosis genome with whole-cell lysate and assaying changes in levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might
INSTITUTE
Weill Cornell Medical College
DEPARTMENT
Microbiology and Immunology
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 Avenue, New York, NY
EMAIL
kyr9001@med.cornell.edu
PHONE
-
NUM_GROUPS
3 replicates X 3 timepoints
STUDY_COMMENTS
The timepoints in the datafiles refer the amount of time (in minutes) that each was incubated with lysate.The units for 'mzmed' are mass/charge.The units for are seconds (retention time).The units for all the other data columns in the are arbitrary; they are integrated peak counts.In this study, Rv1713 was with lysate with and without 1mM GTP added as a co-factor.
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3280
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in M. tuberculosis genome with whole-cell lysate and assaying changes in levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might
INSTITUTE
Weill Cornell Medical College
DEPARTMENT
Microbiology and Immunology
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 Avenue, New York, NY
EMAIL
kyr9001@med.cornell.edu
PHONE
-
NUM_GROUPS
3 replicates X 3 timepoints
STUDY_COMMENTS
The timepoints in the datafiles refer the amount of time (in minutes) that each was incubated with lysate.The units for 'mzmed' are mass/charge.The units for are seconds (retention time).The units for all the other data columns in the are arbitrary; they are integrated peak counts.In this study, Rv1713 was with lysate with and without 1mM GTP added as a co-factor.
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3244
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in M. tuberculosis genome with whole-cell lysate and assaying changes in levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might
INSTITUTE
Weill Cornell Medical College
DEPARTMENT
Microbiology and Immunology
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 Avenue, New York, NY
EMAIL
kyr9001@med.cornell.edu
PHONE
-
NUM_GROUPS
3 replicates X 3 timepoints
STUDY_COMMENTS
The timepoints in the datafiles refer the amount of time (in minutes) that each was incubated with lysate.The units for 'mzmed' are mass/charge.The units for are seconds (retention time).The units for all the other data columns in the are arbitrary; they are integrated peak counts.In this study, Rv1713 was with lysate with and without 1mM GTP added as a co-factor.
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3801
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in M. tuberculosis genome with whole-cell lysate and assaying changes in levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might
INSTITUTE
Weill Cornell Medical College
DEPARTMENT
Microbiology and Immunology
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 Avenue, New York, NY
EMAIL
kyr9001@med.cornell.edu
PHONE
-
NUM_GROUPS
3 replicates X 3 timepoints
STUDY_COMMENTS
The timepoints in the datafiles refer the amount of time (in minutes) that each was incubated with lysate.The units for 'mzmed' are mass/charge.The units for are seconds (retention time).The units for all the other data columns in the are arbitrary; they are integrated peak counts.In this study, Rv1713 was with lysate with and without 1mM GTP added as a co-factor.
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3311
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in M. tuberculosis genome with whole-cell lysate and assaying changes in levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might
INSTITUTE
Weill Cornell Medical College
DEPARTMENT
Microbiology and Immunology
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 Avenue, New York, NY
EMAIL
kyr9001@med.cornell.edu
PHONE
-
NUM_GROUPS
3 replicates X 3 timepoints
STUDY_COMMENTS
The timepoints in the datafiles refer the amount of time (in minutes) that each was incubated with lysate.The units for 'mzmed' are mass/charge.The units for are seconds (retention time).The units for all the other data columns in the are arbitrary; they are integrated peak counts.In this study, Rv1713 was with lysate with and without 1mM GTP added as a co-factor.
To understand the contribution of adipose tissue fatty acid oxidation to metabolism, we generated mice with an adipose-specific knockout of carnitine 2 (CPT2A?/?), an obligate step in mitochondrial long-chain fatty acid CPT2A?/? mice became hypothermic after an acute cold challenge, and CPT2A?/? adipose tissue (BAT) failed to upregulate thermogenic genes in response to stimulation. The adipose-specific loss of CPT2 resulted in diet-dependent in adiposity but did not result in changes in body weight on low- or high-fat Additionally, CPT2A?/? mice had suppressed high-fat diet-induced oxidative and inflammation in visceral white adipose tissue (WAT); however, high-fat glucose intolerance was not improved. These data show that fatty acid oxidation required for cold-induced thermogenesis in BAT and high-fat diet-induced stress and inflammation in WAT.
INSTITUTE
University of Michigan
DEPARTMENT
Biological Chemistry(Johns Hopkins University School of Medicine)
LABORATORY
Wolfgang Lab(Johns Hopkins University School of Medicine)
LAST_NAME
Wolfgang
FIRST_NAME
Michael
ADDRESS
733 North Broadway, Suite G49 Baltimore, MD 21205-2196
EMAIL
mwolfga1@jhmi.edu
PHONE
443-287-7680
NUM_GROUPS
2
TOTAL_SUBJECTS
16
STUDY_COMMENTS
(CPT2A?/?) stands for Carnitine palmitoyltransferase 2 knock out
Metabolic analysis of Parp1 ko/wt Saline & Bleo Mouse Lung Fiboblasts and Human & Normal Lung Fiboblasts (Part 2)
STUDY_TYPE
Glycolysis/TCA/Nucleotide analysis. Ceramide analysis for parp1 wild type lung after saline or bleomycin treatment.
STUDY_SUMMARY
This study is a part of series performed for the same researcher through grant program, so the publication is relevant reference for other studies ST000183)This specific experiment is a small pilot study to establish method it includes four biological replicas of identical cell cultures after the treatment and a single tissue sample.
This study is a part of series performed for the same researcher through pilot/feasibility grant program, so the publication is relevant reference for other studies (ST000199)This specific experiment is a pilot study to compare the metabolism of cells transformed using empty vector against cells transformed with vector carrying short hairpin RNA (shRNA) targeted to silence isocitrate dehydrogenase-1 (IDH1) gene.
The goal of the study was to compare the influence of Ileal pouch-anal (IPAA) surgical treatment on patients with ulcerative colitis (UC) vs those familial adenomatous polyposis (FAP). Stool samples were obtained at the time clinic visit, immediately frozen and stored at -80oC until the assay. There no exclusion criteria.
Small airway epithelial cell (SAEC) (Lonza Walkersville, Inc., MD) were grown according to the manufacturer's instructions in growth medium (SAGM) containing 0.03 mg/ml bovine pituitary extract (BPE), 0.5 µg/ml hydrocortisone, 0.5 ng/ml hEGF, 0.5 µg/ml epinephrine, 10 µg/ml transferrin, 5 µg/ml insulin, 0.1 ng/ml retinoic acid, 6.5ng/ml triiodothyronine, 50 µg/ml gentamicin and 50ng/ml Amphotericin-B, and 0.5 mg/ml bovine serum albumin (BSA, fatty acid free). When SAE grew to around 80 to 90% confluence, the cells were put into basal medium not supplemented with growth factors 3hours. Then the cell monolayers were infected with naïve hMPV at multiplicity of infection (MOI) of 3 to certain time. The supernatant was saved and cells were harvested and stored exactly according to the protocol provided by University of Michigan Metabolomics Core Facility for metabolomics analysis. 50mM ammonium acetate in water was used for rinse buffer.
Small airway epithelial cell (SAEC) (Lonza Walkersville, Inc., MD) were grown according to the manufacturer's instructions in growth medium (SAGM) containing 0.03 mg/ml bovine pituitary extract (BPE), 0.5 µg/ml hydrocortisone, 0.5 ng/ml hEGF, 0.5 µg/ml epinephrine, 10 µg/ml transferrin, 5 µg/ml insulin, 0.1 ng/ml retinoic acid, 6.5ng/ml triiodothyronine, 50 µg/ml gentamicin and 50ng/ml Amphotericin-B, and 0.5 mg/ml bovine serum albumin (BSA, fatty acid free). When SAE grew to around 80 to 90% confluence, the cells were put into basal medium not supplemented with growth factors 3hours. Then the cell monolayers were infected with naïve hMPV at multiplicity of infection (MOI) of 3 to certain time. The supernatant was saved and cells were harvested and stored exactly according to the protocol provided by University of Michigan Metabolomics Core Facility for metabolomics analysis. 50mM ammonium acetate in water was used for rinse buffer.
Pilot Study 13C flux effects when RhoC or RhoA perturbed (13C BCs)
STUDY_TYPE
13C mass isotopomer analysis (flux studies)
STUDY_SUMMARY
Rho-GTPases are small GTP-binding proteins that contribute to the epithelial-to-mesenchymal transition by regulating several cellular processes including organization of the actin cytoskeleton, cell motility, transcription, and cell proliferation. Overexpression of RhoC-GTPases (RhoC) in breast cancer has been implicated in poor disease prognosis due to increased cancer cells invasion, migration, and motility, which warranted its consideration as a therapeutic target for inhibiting breast cancer metastasis. Using silencing RNA (siRNA) molecules to knockdown RhoC expression is a promising approach to inhibit breast cancer metastases.
INSTITUTE
University of Michigan
DEPARTMENT
Internal Medicine
LABORATORY
Merajver Lab
LAST_NAME
Wynn
FIRST_NAME
Michelle
ADDRESS
University Michigan, 2900 Huron Parkway, Ann Arbor, MI 48105
This experiment was performed using the following cohorts: 1) healthy controls, patients with scleroderma at low risk for pulmonary hypertension, 3) pateints scleroderma at high risk for pulmonary hypertension. Whole blood was drawn into stop soilution (1:1 ratio) at rest and again at peak exercise for each subject.
In vitro study with AML cell lines that are treated with different concentrations of cytarabine (nucleoside analog). 8 AML cell lines were incubated for 24hr with 0uM, 1uM and 10uM ara-C. After 24hr the cells were washed and pellets were stored in -80°C for genomic and metabolomic analysis.
Maize plants were transformed with endosperm-specific PPDK RNAi knockout constructs to alter starch/protein ratios. Metabolite pool comparisons will be examined from sibling kernels harvested from segregating ears.
Maize plants were grown under three different temperature regimes: 1) normal day / normal night; 2) hot day / normal night; 3) hot day / hot night. Kernels from developing ears were taken 14, 16, 18, 22, 26 and 40 days after pollination.
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LABORATORY
Stewart
LAST_NAME
Stewart
FIRST_NAME
Jon D.
ADDRESS
102 Leigh Hall
EMAIL
jds2@chem.ufl.edu
PHONE
352-846-0743
NUM_GROUPS
3
TOTAL_SUBJECTS
47
STUDY_COMMENTS
Normal day / normal night (17 samples); Hot day / normal night (14 samples); Hot day / hot night (17 samples)
LC-MS Based Approaches to Investigate Metabolomic Differences in the Urine of Young Women after Drinking Cranberry Juice or Apple Juice
STUDY_TYPE
drug dosage
STUDY_SUMMARY
Eighteen healthy female college students between 21-29 years old with a normal BMI of 18.5-25 were recruited. Each subject was provided with a list of foods that contained significant amount of procyanidins, such as cranberries, apples, grapes, blueberries, chocolate and plums. They were advised to avoid these foods during the 1-6th day and the rest of the study. On the morning of the 7th day, a first-morning baseline urine sample and blood sample were collected from all human subjects after overnight fasting. Participants were then randomly allocated into two groups (n=9) to consume cranberry juice or apple juice. Six bottles (250 ml/bottle) of juice were given to participants to drink in the morning and evening of the 7th, 8th, and 9th day. On the morning of 10th day, all subjects returned to the clinical unit to provide a first-morning urine sample after overnight fasting. The blood sample was also collected from participants 30 min later after they drank another bottle of juice in the morning. After two-weeks of wash out period, participants switched to the alternative regimen and repeated the protocol. One human subject was dropped off this study because she missed part of her appointments. Another two human subjects were removed from urine metabolomics analyses because they failed to provide required urine samples after juice drinking.The present study aimed to investigate overall metabolic changes caused by procyanidins concentrates from cranberries and apples using a global LCMS based metabolomics approach. All plasma and urine samples were stored at -80oC until analysis.
LC-MS Based Approaches to Investigate Metabolomic Differences in the Plasma of Young Women after Drinking Cranberry Juice or Apple Juice
STUDY_TYPE
drug dosage
STUDY_SUMMARY
Eighteen healthy female college students between 21-29 years old with a normal BMI of 18.5-25 were recruited. Each subject was provided with a list of foods that contained significant amount of procyanidins, such as cranberries, apples, grapes, blueberries, chocolate and plums. They were advised to avoid these foods during the 1-6th day and the rest of the study. On the morning of the 7th day, a first-morning baseline urine sample and blood sample were collected from all human subjects after overnight fasting. Participants were then randomly allocated into two groups (n=9) to consume cranberry juice or apple juice. Six bottles (250 ml/bottle) of juice were given to participants to drink in the morning and evening of the 7th, 8th, and 9th day. On the morning of 10th day, all subjects returned to the clinical unit to provide a first-morning urine sample after overnight fasting. The blood sample was also collected from participants 30 min later after they drank another bottle of juice in the morning. After two-weeks of wash out period, participants switched to the alternative regimen and repeated the protocol. One human subject was dropped off this study because she missed part of her appointments. Another two human subjects were removed from urine metabolomics analyses because they failed to provide required urine samples after juice drinking.The present study aimed to investigate overall metabolic changes caused by procyanidins concentrates from cranberries and apples using a global LCMS based metabolomics approach. All plasma and urine samples were stored at -80oC until analysis.
Mechanisms of Metabolic Cycles in Diapausing Flesh Fly by Metabolomics Approach
STUDY_TYPE
time course
STUDY_SUMMARY
Insects use diapause, a programmed period of dormancy, to avoid stressful times of the year and to exploit seasonal times of resource availability. Because most diapausing insects do not feed, they must live off their body reserves for several months and the proper use of metabolic reserves is critical for surviving diapause and performing after diapause termination. Across multiple insects, metabolic depression during diapause has been associated with a switch from aerobic metabolism to facultative anaerobic metabolism, despite insects not suffering environmental oxygen limitation. While metabolic rates are depressed during diapause overall to save energy, some insects show regular cyclical bouts of higher metabolic activity during diapause. The functional importance of these metabolic cycles and the mechanisms underlying these cycles are still unknown, but they may be critical for properly maintaining the balance between energy states and purge the accumulation of anaerobic metabolic byproducts. In the present study, we will test the hypothesis that periodic cycles of increased metabolism during insect diapause are associated with both regenerating organismal energetic states, particularly ATP that may decline during metabolic depression, and for purging metabolites associated with anaerobic metabolism. We will use a combination of non-targeted uHPLC-MS/MS metabolomics and targeted NMR-spectroscopy to identify and quantify metabolites that are altered during the cycles in diapausing pupae of the flesh fly, Sarcophaga crassipalpis. This work will allow us to propose specific biochemical and cellular hypotheses for the regulation of cyclic releases from metabolic depression in diapausing insects. Our work may not only reveal the physiological mechanisms regulating metabolic cycles during diapause in flesh fly, but also provide insight to understand the regulation of similar metabolic cycles in mammalian hibernators (i.e., periodic arousal), and also provide insights into how these cycles could be exploited to disrupt the diapause of insect pests.
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LAST_NAME
Chen
FIRST_NAME
Chao
ADDRESS
Department of Entomology and Nematology, Bldg. 970, 1881 Natural Area Dr., Gainesville, FL 32611
Cecal samples were isolated directly from the ceca of dissected chickens that were either experimentally infected with C. jejuni DRH212 or mock-infected with PBS. Cecal samples were re-suspended in Life Technologies 1X PBS based on weight of sample (1 ml/100 mg = 10-1 dilution) and stored at -80C.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
GBM cell lines were plated onto 10 cm dishes at 100,000-200,000 cells per dish and allowed to grow for 3-4 days until confluency reached 50-70%. Media for all cell lines was DMEM with 10% FBS including 25 mM glucose, 6.2 mM glutamine and 200 uM Oleic Acid (conjugated to BSA). 1-2 hours prior to tracer incubation, media was aspirated and fresh media was used. Immediately prior to tracer incubation, media was again aspirated and then cells were washed with warm PBS to remove unlabeled metabolites. Cells were then incubated with labeled tracer (DMEM with 10% FBS including 25 mM Uniformly labeled 13C-6 glucose, 6.2 mM unlabeled glutamine and 200 uM unlabeled oleic acid). After 2 hours of incubation with tracer, media was aspirated, cells were quickly washed with 15 mL DI water, quenched with liquid nitrogen and then stored at -80oC until analysis.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Human fecal bile acid profiles before and after fecal transplant
STUDY_SUMMARY
Understand the bile acid profiles from the feces of fecal microbiota transplant FMT patients that successfully recover from recurrent C. difficile infection. Submitting fecal samples from patients prior to their FMT and post FMT. Interested in the bile acid profiles of the donor stool that is used in successful transplants. Bile acids are important for C. difficile spore germination and outgrowth.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Early in life exposure studies on human and mouse samples
STUDY_SUMMARY
Experiment1: 2 day old baby mice were exposed to hyperoxia (75% O2) continuously for 7 days. Control baby mice were housed in room air (normoxia). Plasma and bronchoalveolar lavage fluid (BALF) were harvested after 7 days of exposure (on Day of life 9). Experiment2: 2 day old baby mice were exposed to room air or hyperoxia for 14 days and subsequently treated with RV1 or sham.Plasma was collected 5 days after treatment. Human tracheal aspirates were collected from prematurely born infants undergoing mechanical ventilation for respiratory distress syndrome in the first week of life.Tracheal aspirate supernatants are submitted for the assay. We would like to measure adenosine, AMP, ADP and ATP levels.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
13C mass isotopomer analysis (LCMS flux studies) MLL-AF9 (part I)
STUDY_TYPE
1,2-13C2 Flux analysis
STUDY_SUMMARY
"How cancer cells adapt to metabolically adverse conditions in patients and strive to proliferate is a fundamental question in cancer biology. Here we show that AMP-activated protein kinase (AMPK), a metabolic checkpoint kinase, confers metabolic stress resistance to leukemia-initiating cells (LICs) and promotes leukemogenesis. Upon dietary restriction, MLL-AF9-induced murine acute myeloid leukemia (AML) activated AMPK and maintained leukemogenic potential. AMPK deletion significantly delayed leukemogenesis and depleted LICs by reducing the expression of glucose transporter 1 (Glut1), compromising glucose flux, and increasing oxidative stress and DNA damage. LICs were particularly dependent on AMPK to suppress oxidative stress in the hypoglycemic bone marrow environment. Strikingly, AMPK inhibition synergized with physiological metabolic stress caused by dietary restriction and profoundly suppressed leukemogenesis. Our results indicate that AMPK protects LICs from metabolic stress and that combining AMPK inhibition with physiological metabolic stress potently suppresses AML by inducing oxidative stress and DNA damage. Research is published: http://www.sciencedirect.com/science/article/pii/S1934590915003744 "
INSTITUTE
University of Michigan
DEPARTMENT
Molecular and Human genetics (Baylor College of Medicine)
LABORATORY
Nakada Lab (Baylor College of Medicine)
LAST_NAME
Saitoh
FIRST_NAME
Yusuke
ADDRESS
Houston, TX
EMAIL
Yusuke.Saitoh@bcm.edu
PHONE
713-798-1175
NUM_GROUPS
7
TOTAL_SUBJECTS
18
STUDY_COMMENTS
1. Collect leukemia cells from MLL-AF9 leukemia mouse bone marrow. 2. Leukemia cell were cultured in RPMI1640 medium for 16hr. 3. Cell pellets were resuspend in pre-warmed labeling medium containing 1,2-13C2-glucose(2g/L) and incubated for 5min (sample 5) or 60min(sample 60).
Metabolome of three Vancomycin-intermediate Staphylococcus aureus (VISA) mutants compared with the parent strain MM66
STUDY_SUMMARY
Vancomycin-intermediate Staphylococcus aureus (VISA) evolve in a strain-specific manner and acquire mutations that lead to alterations in cell wall metabolism that reduce susceptibility to vancomycin. We had earlier isolated several VISA mutant strains of the clinical hVISA strain MM66. This study is aimed at analyzing the metabolome of these mutants in comparison to the parent strain.
INSTITUTE
Oklahoma State University, Stillwater, OK
LAST_NAME
Gustafson
FIRST_NAME
John
ADDRESS
246C Noble Research Center Oklahoma State University Stillwater, OK 74078-3035
Muscle Clock knock out mice metabolic changes (iMSBmal1-Exp1)
STUDY_TYPE
Regular
STUDY_SUMMARY
My lab studies the function of the molecular clocks in skeletal muscle. We have an inducible genetic mouse model (C57Bl6 background) in which we knock out the core clock gene, Bmal1, only in adult skeletal muscle after treatment with tamoxifen. We have found that the mice maintain body mass but lose fat mass at 10 weeks after loss of Bmal1. We have done expression profiling on the skeletal muscles and gene expression changes (insulin signaling, CHO metabolism, fat metabolism) suggest significant changes in substrate metabolism. To analyze TCA, CHO metabolites we have collected gastrocnemius muscles from these mice following instructions from Dr. Burant. Mice were anaesthetized with isoflurane, the gastrocnemius muscle dissected and flash frozen with tongs cooled with liquid N2. They have been stored in cryovials in our -80 freezer for 2 months.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Comparison of Metabolites Variation and Antiobesity Effects of a Mixture of Cudrania tricuspidata, Lonicera caerulea, and the Soybean According to Fermentation in vitro and in vivo
STUDY_SUMMARY
We used ultra-performance-liquid-chromatography with quadrupole-time-of-flight mass spectrometry to study the changes in metabolites in the mixture of Cudrania tricuspidata, Lonicera caerulea, and soybean (CLM) during fermentation. Additionally, the antiobesity effects of CLM and fermented-CLM (FCLM) were studied based on the analysis of plasma from high-fat diet (HFD)-fed mice. The levels of cyanidin and the glycosides of luteolin, quercetin, and cyanidin derived from L. caerulea were decreased, whereas the levels of luteolin and quercetin were increased during fermentation. Isoflavone glycosides and soyasaponins originating from the soybean were decreased, whereas their aglycones such as daidzein, glycitein, and genistein were increased. As for prenylated flavonoids from C. tricuspidata, these metabolites were decreased at the early stage of fermentation, and were increased at end of the fermentation. In terms of the functional food product, various metabolites derived from diverse natural products in CLM had complementary effects and demonstrated higher antioxidant and pancreatic lipase inhibition activities by fermentation; these activities were closely related to flavonoid aglycones including genistein, daidzein, glycitein, luteolin, and quercetin. In vivo experiment, several clinical parameters affected by HFD were remarkably improved by the administration of either CLM or FCLM, but there was a difference in the antiobesity effects. The levels of lysoPCs with C20:4, C16:0, and C22:6 were significantly attenuated by CLM administration, while the attenuated levels of lysoPCs with C20:4 and C18:2 were significantly restored by FCLM administration. These metabolites may explain the above-mentioned differences in antiobesity effects. Although only the changes in plasma lysophospholipids could not fully explain antiobesity effects between non-fermented and fermented plant mixtures from our results, we suggest that metabolomics approach could provide a way to reveal the metabolite alterations in the complex fermentation process and understand the differences or changes in bioactivity according to fermentation.
INSTITUTE
Konkuk university
LAST_NAME
Suh
FIRST_NAME
Dong Ho
ADDRESS
Neong-Dong-ro 120, Seoul, Kwang-Gin-gu, 05029, Korea, South
Single treatment gene impact on Arabidopsis metabolites
STUDY_SUMMARY
This experiment aims to measure the impact of the genes that have been introduced into WT lines and compare the metabolic profiling of these plants with WT control plants. Compounds of particular intereset for this study include pyruvate, fumarate, malate, glyoxylate, anthocyanin, carotenes, and lipid compounds.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
This experiment tested the affects of different diets on mice esophagus metabolites. The diets ranged from zinc sufficient to zinc deficient and a third group that included zinc deficient mice that were put back on zinc sufficient diets.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Effects of Zinc on GI tract metabolites (Part 2: Prostate)
STUDY_SUMMARY
This experiment tested the affects of different diets on mice prostate metabolites. The diets ranged from zinc sufficient to zinc deficient and a third group that included zinc deficient mice that were put back on zinc sufficient diets.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
This experiment aimed to see the effects of Giardia Intestinalis on the small intestine of mice. The metabolites of the proximal and distal ends of the small intestine of healthy mice were compared to those of mice who had been infected with Giardia intestinalis for 7 days.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Metabolomics of bovine uterine fluid at the onset of conceptus elongation
STUDY_TYPE
Prospective cohort study
STUDY_SUMMARY
The objective is to investigate changes in metabolomics of uterine lumen content of lactating dairy cows associated with the onset of conceptus (embryo and associated membranes) elongation. Lactating dairy cows had estrous cycles synchronized and were subjected to induced ovulation and timed artificial insemination (AI). The day of AI was considered study d 0. On d 15, uteri were flushed by transcervical catheterization and infusion of 20 mL of phosphate buffered solution with 0.1% of polyvinyl acetate. Recovered conceptuses were classified based on morphology/length as ovoid (OV; 1-4 mm), tubular (TUB; 5-19 mm) and filamentous (FIL; 20-85 mm). The first 20 mL infused in the uterus were recovered, placed in conical tubes and centrifuged at 2,000 × g at 4ᵒC. The supernatant was collect, aliquoted and stored at -80ᵒC for later analyses of fluid composition, including measurement of IFN-τ concentration. Cows with no conceptus recovered and no detection of IFN-τ in uterine flushing were considered as nonpregnant (NPREG). The experimental design was then considered a prospective cohort study with 4 independent groups (NPREG, OV, TUB, and FIL). The additional 5th group represents a specific physiological condition of cows within the study and it will be compared to TUB and FIL groups combined, working as a pilot study for future research.
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LABORATORY
Laboratory of Reproduction and Nutrition of Dairy Cows
Metabolomics Approach to Allograft Assessment in Liver Transplantation
STUDY_TYPE
Retrospective analysis of biobanked liver tissue from organ donors
STUDY_SUMMARY
This pilot study is designed to apply several types of metabolomic analysis for liver allograft assessment with the aim of identifying candidate biomarkers for allograft function and to develop a methodology that could be applied to larger scale studies. The three main categories of metabolomic analysis are reflected in each of the specific aims, including a targeted profiling of central carbon metabolism, open lipidomic and metabolomic profiling for hypothesis generation and MALDI-IMS for tissue-based spatial analysis. Each of these approaches offers potential benefits that could be optimized in a protocol for larger scale studies depending the results of the pilot investigations.
INSTITUTE
Ochsner Multi-Organ Transplant Institute
DEPARTMENT
SECIM
LABORATORY
Abdominal Organ Transplantation
LAST_NAME
Seal
FIRST_NAME
John
ADDRESS
1514 Jefferson Highway, New Orleans, LA 70121
EMAIL
John.Seal@ochsner.org
PHONE
504-232-4253
NUM_GROUPS
3
TOTAL_SUBJECTS
Targeted analysis and open profiling: Control group - standard criteria donor (N=15); Experimental group - donation-after-cardiac-death donors (N=10). MALDI-IMS - standard criteria donor (N=10)
This experiment aimed to discover the effects of metformin on mouse liver and kidney tissue. The effects were seen by comparing the liver of the metformin group to the liver of a control group of mice treated given saline solution.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Renal metabolic pathways indicating ischemic or inflammatory changes
STUDY_SUMMARY
Tissues were acquired from kidkeys that were deemed unsuitable for transplant and were then analyzed by the lab through normothermic machine perfusion. They were perfused with either whole blood perfusate or with packed red blood cell perfusate. These tissues' metabolic pathways were then analyzed for markers of ischemic or inflammatory responses in the renal tissue
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Modification of metabolites by gut microbiota in response to diet
STUDY_SUMMARY
This experiment is looking at effects of diets on rats. Specifically how those diets might alter metabolites that could be modified by gut microbiota and in particular indoles and bile salts.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Effects of dietary supplement on hamster metabolism
STUDY_SUMMARY
This experiment aims to analyze spent media from a protein over-expression system. The treatment was a lipid supplement given to hamsters. The spent media was then analyzed to see how the lipid supplement affected lipid metabolism.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
The Development of Metabolomic Markers in African Bermudagrass (C. transvaalensis) for Sting Nematode (Belonolaimus longicaudatus) Response
STUDY_TYPE
Disease response in terms of nematode reproduction and root weight
STUDY_SUMMARY
The objective of the proposed pilot study is to identify metabolites up- and down-regulated in African bermudagrass that are tolerant and sensitive to the sting nematode and develop metabolomic markers for the highest expressed metabolites associated with tolerance. Future work will include additional accessions and species of bermudagrass, and testing under field conditions. Bermudagrass accessions identified as tolerant or sensitive by Pang et al. (2011) will be assessed under controlled greenhouse conditions to identify metabolites linked to sting nematode tolerance. Nematode response will be quantified through determination of root length and weight and the number of nematodes present 136 days after inoculation. Higher root length and weight indicate tolerance or resistance. Higher nematode counts indicate greater reproduction (i.e. a susceptible plant), while lower counts indicate that the accession may have some resistance. Metabolites from root tissue of these accessions will be compared to identify those associated with tolerance/resistance, and those that are associated with nematode infestation by comparing inoculated plants to uninoculated controls. Metabolomic markers will then be developed for the metabolites associated with tolerance/resistance. These markers will be used to guide future screening of bermudagrass accessions for breeding nematode-tolerant or -resistant varieties.
Metabolite comparison of mouse gastric tissue and glands
STUDY_SUMMARY
The goal of this project was to compare the metabolite profiles of the: mouse gastric antrum and the mouse gastric corpus, the mouse gastric antrum and the mouse gastric antrum isolated glands, and the mouse gastric corpus and the mouse gastric corpus isolated glands.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Broad Spectrum MS analysis of mouse hypothalmus from Anxiety Prone HSV-Latently Infected Obese Mice
STUDY_TYPE
Broad Spectrum LCMS
STUDY_SUMMARY
Brain tissue samples for metabolomics experiments were generated in the following manner: 3-week old mice were placed on a 10% low fat (LF) diet and acclimated for one week prior to intranasal HSV-1 infection or mock infection with PBS. Fourteen days post-infection mice were randomized to either a 45% high fat diet (HF) or remained on the LF diet. Eight weeks post-diet transition, mice were euthanized and brain tissue samples were collected and processed for metabolomics.
Broad Spectrum MS analysis of mouse hippocampus from Anxiety Prone HSV-Latently Infected Obese Mice
STUDY_TYPE
Broad Spectrum LCMS
STUDY_SUMMARY
Brain tissue samples for metabolomics experiments were generated in the following manner: 3-week old mice were placed on a 10% low fat (LF) diet and acclimated for one week prior to intranasal HSV-1 infection or mock infection with PBS. Fourteen days post-infection mice were randomized to either a 45% high fat diet (HF) or remained on the LF diet. Eight weeks post-diet transition, mice were euthanized and brain tissue samples were collected and processed for metabolomics.
Broad Spectrum MS analysis of mouse microglia cells from Anxiety Prone HSV-Latently Infected Obese Mice
STUDY_TYPE
Broad Spectrum LCMS
STUDY_SUMMARY
A mouse model of obese HSV-1 latent infection was developed. Broad spectrum metabolomics analysis was performed to better understand the metabolomic profile of microglia cells and to compare this metabolomics profile with that of the hippocampus, hypothalamus, and peripheral blood mononuclear cells. Microglia cell samples for metabolomics experiments were generated in the following manner: 3-week old mice were placed on a 10% low fat (LF) diet and acclimated for one week prior to intranasal HSV-1 infection or mock infection with PBS. Fourteen days post-infection mice were randomized to either a 45% high fat diet (HF) or remained on the LF diet. Eight weeks post-diet transition, mice were euthanized and microglia cell samples were collected and processed for metabolomics.
Characterization and Plasticity of the Metabolome in Peripheral Cells in Bipolar I Disorder
STUDY_TYPE
Broad Spectrum LCMS
STUDY_SUMMARY
Patients with Bipolar I Disorder (BPI) and matched non-affected controls were recruited. Males and females from all races and ethnicities between the ages of 19-65 participated in the research. Skin biopsies were obtained and fibroblasts were isolated from each of these biopsies. A total of 1 x 〖10〗^7 fibroblasts cells were used for metabolomics. Cell pellets were flash frozen in liquid nitrogen and shipped on dry ice to the NIH Eastern Regional Comprehensive Metabolomic Resource Core at RTI International in North Carolina. Metabolomics will be determined using a broad spectrum metabolomics protocol by RTI
Associations between 69 Sphingolipids and Emphysema, Chronic Bronchitis, Exacerbations, and FEV1/FVC
STUDY_TYPE
Association Study
STUDY_SUMMARY
One hundred twenty-nine current and former smokers from the COPDGene cohort had 69 distinct sphingolipid species detected in plasma by targeted mass spectrometry. Of these, 23 were also measured in 131 plasma samples (117 independent subjects) using an untargeted platform in an independent laboratory. Regression analysis with adjustment for clinical covariates, correction for false discovery rate, and metaanalysis were used to test associations between COPD subphenotypes and sphingolipids. Peripheral blood mononuclear cells were used to test associations between sphingolipid gene expression and plasma sphingolipids.
Broad Spectrum MS analysis of mouse peripheral blood mononuclear cells (PBMC) from Anxiety Prone HSV-Latently Infected Obese Mice
STUDY_TYPE
Broad Spectrum LCMS
STUDY_SUMMARY
Mononuclear cell samples for metabolomics experiments were generated in the following manner: 3-week old mice were placed on a 10% low fat (LF) diet and acclimated for one week prior to intranasal HSV-1 infection or mock infection with PBS. Fourteen days post-infection mice were randomized to either a 45% high fat diet (HF) or remained on the LF diet. Eight weeks post-diet transition, mice were euthanized and mononuclear cell samples were collected and processed for metabolomics.
Labeling of cells was carried out in triplicate with each sample containing 35e6. Cells were deprived of glucose or glutamine for 1 h then resuspended in 10mM [13C1,2] D-glucose labeled or 4 mM [13C5]-U-glutamine labeled medium, respectively. At this time cells were also activated with 5 ug/ml anti-CD3 and anti-CD28. Cells were labeled (and activated) for 16 h when samples were spun down, and cells were resuspended in 200 ul ice cold methanol. For this part of the experiment, the spent medium was collected for analysis. All samples were immediately stored in -80oC.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research
LABORATORY
Core Facilities Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
There are 4 germfree controls and 4 germfree with bacteria. After treatment, the mouse stool samples were collected at different timepoints: day 0, day 10, day 26, day 47, and day 61 or 70. Place the stool samples into liquid nitrogen after they were collected, then stored in -80oC.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Measure change in metabolites based on diet and feeding status
STUDY_TYPE
Regular
STUDY_SUMMARY
Flies were fed a normal diet or high-sugar (30% sucrose) diet for 10 days. Flies of each diet were flash frozen in liquid nitrogen as sated (refed for 3hrs on 400mM D-glucose) or after fasting for 24hrs. Heads and bodies were separated using a sieve-system and placed immediately on dry ice (total time app. 1min). We collected 50 heads per condition (4 conditions total) and 5 biological replicates
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Measure change in metabolites based on diet and feeding status (part II)
STUDY_TYPE
Regular
STUDY_SUMMARY
Flies were fed a normal diet or high-sugar (30% sucrose) diet for 10 days. Flies of each diet were flash frozen in liquid nitrogen as sated (refed for 3hrs on 400mM D-glucose) or after fasting for 24hrs. Heads and bodies were separated using a sieve-system and placed immediately on dry ice (total time app. 1min). We collected 50 heads per condition (4 conditions total) and 5 biological replicates
Temporal metabolomic responses of cultured HepG2 liver cells to high fructose and high glucose exposures
STUDY_SUMMARY
High fructose consumption has been implicated with deleterious effects on human health, including hyperlipidemia elicited through de novo lipogenesis. However, more global effects of fructose on cellular metabolism have not been elucidated. In order to explore the metabolic impact of fructose-containing nutrients, we applied both GC-TOF and HILIC-QTOF mass spectrometry metabolomic strategies using extracts from cultured HepG2 cells exposed to fructose, glucose, or fructose + glucose. Cellular responses were analyzed in a time-dependent manner, incubated in media containing 5.5 mM glucose + 5.0 mM fructose in comparison to controls incubated in media containing either 5.5 mM glucose or 10.5 mM glucose. Mass spectrometry identified 156 unique known metabolites and a large number of unknown compounds, which revealed metabolite changes due to both utilization of fructose and high-carbohydrate loads independent of hexose structure. Fructose was shown to be partially converted to sorbitol, and generated higher levels of fructose-1-phosphate as a precursor for glycolytic intermediates. Differentially regulated ratios of 3-phosphoglycerate to serine pathway intermediates in high fructose media indicated a diversion of carbon backbones away from energy metabolism. Additionally, high fructoseconditions changed levels of complex lipids toward phosphatidylethanolamines. Patterns of acylcarnitines in response to high hexose exposure (10.5 mM glucose or glucose/fructose combination) suggested a reduction in mitochondrial beta-oxidation.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Temporal metabolomic responses of cultured HepG2 liver cells to high fructose and high glucose exposures
STUDY_SUMMARY
High fructose consumption has been implicated with deleterious effects on human health, including hyperlipidemia elicited through de novo lipogenesis. However, more global effects of fructose on cellular metabolism have not been elucidated. In order to explore the metabolic impact of fructose-containing nutrients, we applied both GC-TOF and HILIC-QTOF mass spectrometry metabolomic strategies using extracts from cultured HepG2 cells exposed to fructose, glucose, or fructose + glucose. Cellular responses were analyzed in a time-dependent manner, incubated in media containing 5.5 mM glucose + 5.0 mM fructose in comparison to controls incubated in media containing either 5.5 mM glucose or 10.5 mM glucose. Mass spectrometry identified 156 unique known metabolites and a large number of unknown compounds, which revealed metabolite changes due to both utilization of fructose and high-carbohydrate loads independent of hexose structure. Fructose was shown to be partially converted to sorbitol, and generated higher levels of fructose-1-phosphate as a precursor for glycolytic intermediates. Differentially regulated ratios of 3-phosphoglycerate to serine pathway intermediates in high fructose media indicated a diversion of carbon backbones away from energy metabolism. Additionally, high fructoseconditions changed levels of complex lipids toward phosphatidylethanolamines. Patterns of acylcarnitines in response to high hexose exposure (10.5 mM glucose or glucose/fructose combination) suggested a reduction in mitochondrial beta-oxidation.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Plasma Metabolomic Profiles Reflective of Glucose Homeostasis in Non-Diabetic and Type 2 Diabetic Obese African-American Women
STUDY_SUMMARY
Insulin resistance progressing to type 2 diabetes mellitus (T2DM) is marked by a broad perturbation of macronutrient intermediary metabolism. Understanding the biochemical networks that underlie metabolic homeostasis and how they associate with insulin action will help unravel diabetes etiology and should foster discovery of new biomarkers of disease risk and severity. We examined differences in plasma concentrations of >350 metabolites in fasted obese T2DM vs. obese non-diabetic African-American women, and utilized principal components analysis to identify 158 metabolite components that strongly correlated with fasting HbA1c over a broad range of the latter (r?=??0.631; p<0.0001). In addition to many unidentified small molecules, specific metabolites that were increased significantly in T2DM subjects included certain amino acids and their derivatives (i.e., leucine, 2-ketoisocaproate, valine, cystine, histidine), 2-hydroxybutanoate, long-chain fatty acids, and carbohydrate derivatives. Leucine and valine concentrations rose with increasing HbA1c, and significantly correlated with plasma acetylcarnitine concentrations. It is hypothesized that this reflects a close link between abnormalities in glucose homeostasis, amino acid catabolism, and efficiency of fuel combustion in the tricarboxylic acid (TCA) cycle. It is speculated that a mechanism for potential TCA cycle inefficiency concurrent with insulin resistance is “anaplerotic stress” emanating from reduced amino acid-derived carbon flux to TCA cycle intermediates, which if coupled to perturbation in cataplerosis would lead to net reduction in TCA cycle capacity relative to fuel delivery.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
G/g and g/a are polymorphisms in the promoter region of the UCP3 gene that leads to the gene being enhanced and an increased chance of obesity in those with this polymorphism.
PUBLICATIONS
Plasma Metabolomic Profiles Reflective of Glucose Homeostasis in Non-Diabetic and Type 2 Diabetic Obese African-American Women
Metabolomic profiles in P. gingivalis cells treated with pABA
STUDY_SUMMARY
Many human infections are polymicrobial in origin, and synergistic interactions among community inhabitants control colonization and pathogenic potential (Murray et al., 2014). However, few interspecies interactions have been functionally dissected at the molecular level or characterized on a systems level. Periodontitis, which is the sixth most prevalent infectious disease worldwide (Kassebaum et al., 2014), is associated with a dysbiotic microbial community, and the keystone pathogen Porphyromonas gingivalis forms synergistic communities with the accessory pathogen Streptococcus gordonii (Lamont and Hajishengallis, 2015). P. gingivalis and S. gordonii communicate through co-adhesion and metabolite perception, and close association between P. gingivalis and S. gordonii results in significant changes in the expressed proteomes of both organisms (Kuboniwa et al., 2012, Hendrickson et al., 2012). Here we show that streptococcal 4 aminobenzoate/para-amino benzoic acid (pABA) is required for maximal accumulation of P. gingivalis in communities with S. gordonii. Exogenous pABA upregulates production of fimbrial interspecies adhesins and of a tyrosine phosphorylation-dependent signaling system in P. gingivalis. Consequently, fimbrial-dependent attachment and invasion of epithelial cells by P. gingivalis is also increased by pABA. Moreover, trans-omics studies performed by proteomics and metabolomics showed that pABA induces metabolic shifts within P. gingivalis, predominantly folate derivative biosynthesis. In a murine oral infection model, pABA increased colonization and survival of P. gingivalis, but did not increase virulence. The results establish streptococcal pABA as a major component of the interspecies S. gordonii-P. gingivalis interaction which regulates distinct aspects of polymicrobial synergy.
Study1 Investigation of metabolomic blood biomarkers for detection of adenocarcinoma lung cancer (training set)
STUDY_SUMMARY
Recently, the National Lung Cancer Screen Trial (NLST) demonstrated that low-dose CT (LDCT) screening could reduce mortality due to lung cancer by 20%. However, LDCT screening is largely hindered by high false-positive rates (96%), particularly in high-risk populations (heavy smokers), due to the low prevalence rates (less than 2%) of malignant tumors and high incidence of benign lung nodules. Consequently, complementary biomarkers that can be used in conjunction with LDCT screening to improve diagnostic capacities and reduce false-positive rates are highly desirable. Preferably, such complementary tools should be noninvasive and exhibit high sensitivity and specificity. The application of “-omic” sciences (genomics, transcriptomics, proteomics, and metabolomics) represents valuable tools for the discovery and validation of potential biomarkers that can be used for detection of NSCLC. Of these omic sciences, metabolomics has received considerable attention for its application in cancer. Metabolomics is the assessment of small molecules and biochemical intermediates (metabolites) using analytic instrumentation. Metabolites in blood are the product of all cellular processes, which are highly responsive to conditions of disease and environment, and represent the final output products of all organs forming a detailed systemic representation of an individual's current physiologic state. In this study, we used an untargeted metabolomics approach using gas chromatography time-of-flight mass spectrometry (GCTOFMS) to analyze the metabolome of serum and plasma samples both collected from the same patients that were organized into two independent case–control studies (ADC1 and ADC2). In both studies, only NSCLC adenocarcinoma was investigated. The overall objectives were to (i) determine whether individual or combinations of metabolites could be used as a diagnostic test to distinguish NSCLC adenocarcinoma from controls and (ii) to determine which, plasma or serum, provides more accurate classifiers for the detection of lung cancer. We developed individual and multimetabolite classifiers using a training test from the ADC1 study and evaluated the performance of the constructed classifiers, individually or in combination, in an independent test/validation study (ADC2). This study shows the potential of metabolite-based diagnostic tests for detection of lung adenocarcinoma. Further validation in a larger pool of samples is warranted.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
SS = Sigma sample and is used as a quality control The first set (ADC1) used for biomarker development consisted of serum and plasma samples obtained from 52 stages I–IV NSCLC adenocarcinoma patients (52 plasma and 49 serum), and 31 healthy controls (31 pairs of serum and plasma) for a total of 163 samples. This set was regarded as the training set for biomarker discovery and classifier development. A second, independent case–control study (ADC2) consisting of serum and plasma samples collected from 43 stage I–IV NSCLC adenocarcinoma patients and 43 healthy controls (total 172 samples) was used as an independent test set for biomarker evaluation. A limitation of this study is the relatively small sample size for each cohort (52 cases, 31 controls for ADC1, and 43 cases and 43 controls for ADC2) because patient variability can be a big factor in smaller studies.
Metabolomic markers of altered nucleotide metabolism in early stage adenocarcinoma (part I)
STUDY_SUMMARY
Lung cancer has been the leading cause of cancer death in the United States and worldwide for many decades. Low dose spiral computerized tomography (LDCT) is likely to become the first approved screening and early detection test in the upcoming year, but it is plagued by a high false-positive rate. There is a need to develop complementary screening and early detection tools. A blood-based "lung cancer" signature is an attractive solution. Given that our knowledge of the molecular biology of smoking-induced lung cancer has dramatically increased over the past few years, this approach is plausible. To date, this effort has been focused on the identification of genomic and proteomic signatures with limited success. A broader strategy that incorporates additional cancer traits is needed. It is well recognized that wide coverage of cellular metabolism in cancer could help provide valuable diagnostic biomarkers and potentially identify molecular drivers of tumorigenesis. Recent advances in mass spectrometry have enabled comprehensive metabolomic analyses of lipids, carbohydrates, amino acids, and nucleotides within a variety of biologic matrices. Early evidence from metabolomic investigation of cancer has identified many altered biochemical profiles. However, to date, there have been few investigations of lung cancer, and most studies have looked at blood plasma or were limited by small sample sizes with mixed histologies. In the current investigation, gas chromatography time-offlight mass spectrometry (GC-TOF) was used to measure 462 lipid, carbohydrate, amino acid, organic acid, and nucleotide metabolites in 39 malignant and nonmalignant lung tissue pairs from current or former smokers with early stage adenocarcinoma. This study cohort represents patient characteristics and tumor histology most likely to be detected with LDCT screening. We hypothesize that identification of cancer-induced cellular and tissue level biochemical changes can offer a robust method for identification of candidate circulating biomarkers and improve our understanding of biochemical changes involved in adenocarcinoma tumorigenesis.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Metabolomic markers of altered nucleotide metabolism in early stage adenocarcinoma (part II)
STUDY_SUMMARY
Lung cancer has been the leading cause of cancer death in the United States and worldwide for many decades. Low dose spiral computerized tomography (LDCT) is likely to become the first approved screening and early detection test in the upcoming year, but it is plagued by a high false-positive rate. There is a need to develop complementary screening and early detection tools. A blood-based "lung cancer" signature is an attractive solution. Given that our knowledge of the molecular biology of smoking-induced lung cancer has dramatically increased over the past few years, this approach is plausible. To date, this effort has been focused on the identification of genomic and proteomic signatures with limited success. A broader strategy that incorporates additional cancer traits is needed. It is well recognized that wide coverage of cellular metabolism in cancer could help provide valuable diagnostic biomarkers and potentially identify molecular drivers of tumorigenesis. Recent advances in mass spectrometry have enabled comprehensive metabolomic analyses of lipids, carbohydrates, amino acids, and nucleotides within a variety of biologic matrices. Early evidence from metabolomic investigation of cancer has identified many altered biochemical profiles. However, to date, there have been few investigations of lung cancer, and most studies have looked at blood plasma or were limited by small sample sizes with mixed histologies. In the current investigation, gas chromatography time-offlight mass spectrometry (GC-TOF) was used to measure 462 lipid, carbohydrate, amino acid, organic acid, and nucleotide metabolites in 39 malignant and nonmalignant lung tissue pairs from current or former smokers with early stage adenocarcinoma. This study cohort represents patient characteristics and tumor histology most likely to be detected with LDCT screening. We hypothesize that identification of cancer-induced cellular and tissue level biochemical changes can offer a robust method for identification of candidate circulating biomarkers and improve our understanding of biochemical changes involved in adenocarcinoma tumorigenesis.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Systemic Metabolomic Changes in Blood Samples of Lung Cancer Patients Identified by Gas Chromatography Time-of-Flight Mass Spectrometry
STUDY_SUMMARY
Lung cancer is a leading cause of cancer deaths worldwide. Metabolic alterations in tumor cells coupled with systemic indicators of the host response to tumor development have the potential to yield blood profiles with clinical utility for diagnosis and monitoring of treatment. We report results from two separate studies using gas chromatography time-of-flight mass spectrometry (GC-TOF MS) to profile metabolites in human blood samples that significantly differ from non-small cell lung cancer (NSCLC) adenocarcinoma and other lung cancer cases. Metabolomic analysis of blood samples from the two studies yielded a total of 437 metabolites, of which 148 were identified as known compounds and 289 identified as unknown compounds. Differential analysis identified 15 known metabolites in one study and 18 in a second study that were statistically different (p-values <0.05). Levels of maltose, palmitic acid, glycerol, ethanolamine, glutamic acid, and lactic acid were increased in cancer samples while amino acids tryptophan, lysine and histidine decreased. Many of the metabolites were found to be significantly different in both studies, suggesting that metabolomics appears to be robust enough to find systemic changes from lung cancer, thus showing the potential of this type of analysis for lung cancer detection.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
TOTAL_SUBJECTS
82
NUM_MALES
20
NUM_FEMALES
62
STUDY_COMMENTS
SS = Sigma sample and is used as a quality control
Long-Chain Fatty Acid Combustion Rate Is Associated with Unique Metabolite Profiles in Skeletal Muscle Mitochondria
STUDY_SUMMARY
Incomplete or limited long-chain fatty acid (LCFA) combustion in skeletal muscle has been associated with insulin resistance. Signals that are responsive to shifts in LCFA β-oxidation rate or degree of intramitochondrial catabolism are hypothesized to regulate second messenger systems downstream of the insulin receptor. Recent evidence supports a causal link between mitochondrial LCFA combustion in skeletal muscle and insulin resistance. We have used unbiased metabolite profiling of mouse muscle mitochondria with the aim of identifying candidate metabolites within or effluxed from mitochondria and that are shifted with LCFA combustion rate. This proof-of-principle study establishes that large-scale metabolomics methods can be applied to organelle-level models to discover metabolite patterns reflective of LCFA combustion, which may lead to identification of molecules linking muscle fat metabolism and insulin signaling. Our results suggest that future studies should focus on the fate of effluxed TCA cycle intermediates and on mechanisms ensuring their replenishment during LCFA metabolism in skeletal muscle.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
The circadian oscillator in Synechococcus elongatus controls metabolite partitioning during diurnal growth
STUDY_SUMMARY
Cyanobacteria are increasingly being considered for use in large-scale outdoor production of fuels and industrial chemicals. Cyanobacteria can anticipate daily changes in light availability using an internal circadian clock and rapidly alter their metabolic processes in response to changes light availability. Understanding how signals from the internal circadian clock and external light availability are integrated to control metabolic shifts will be important for engineering cyanobacteria for production in natural outdoor environments. This study has assessed how “knowing” the correct time of day, via the circadian clock, affects metabolic changes when a cyanobacterium goes through a dark-to-light transition. Our data show that the circadian clock plays an important role in inhibiting activation of the oxidative pentose phosphate pathway in the morning. Synechococcus elongatus PCC 7942 is a genetically tractable model cyanobacterium that has been engineered to produce industrially relevant biomolecules and is the best-studied model for a prokaryotic circadian clock. However, the organism is commonly grown in continuous light in the laboratory, and data on metabolic processes under diurnal conditions are lacking. Moreover, the influence of the circadian clock on diurnal metabolism has been investigated only briefly. Here, we demonstrate that the circadian oscillator influences rhythms of metabolism during diurnal growth, even though light–dark cycles can drive metabolic rhythms independently. Moreover, the phenotype associated with loss of the core oscillator protein, KaiC, is distinct from that caused by absence of the circadian output transcriptional regulator, RpaA (regulator of phycobilisome-associated A). Although RpaA activity is important for carbon degradation at night, KaiC is dispensable for those processes. Untargeted metabolomics analysis and glycogen kinetics suggest that functional KaiC is important for metabolite partitioning in the morning. Additionally, output from the oscillator functions to inhibit RpaA activity in the morning, and kaiC-null strains expressing a mutant KaiC phosphomimetic, KaiC-pST, in which the oscillator is locked in the most active output state, phenocopies a ΔrpaA strain. Inhibition of RpaA by the oscillator in the morning suppresses metabolic processes that normally are active at night, and kaiC-null strains show indications of oxidative pentose phosphate pathway activation as well as increased abundance of primary metabolites. Inhibitory clock output may serve to allow secondary metabolite biosynthesis in the morning, and some metabolites resulting from these processes may feed back to reinforce clock timing.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
The first 4 samples were a test run to see how efficient the analysis was and were run on a lipidomics platform. The next 12 samples were the used in the paper and were the same as the original 4 samples, but they were split into 3 biological replicates and run on the GC platform.
Recently, major efforts have been directed toward early detection of lung cancer through low-dose computed tomography (LDCT) scanning. Data from the National Lung Screening Trial (NLST) suggest that yearly screening with thoracic LDCT scanning for high-risk current and former smokers reduces lung cancer mortality by 20% and total mortality by 7%. However, issues including indeterminate nodules detected by LDCT and radiation exposure impact the practicality of LDCT-based screening on a national and global basis. A blood-based biomarker or multiplexed marker panel that could complement LDCT would represent a major advance in implementing lung cancer screening. Efforts to develop blood-based biomarkers for lung cancer early detection using a variety of methodologies are currently ongoing. Proteomic studies have led to the identification of several candidate markers including pro-surfactantproteinB(pro-SFTPB), a target of a lineage-survival oncogene in lung cancer, NKX2-1.Validation studies using blood samples collected at the time of LDCT screening for lung cancer substantiated the performance of pro-SFTPB. Multivariable logistic regression models were used to evaluate the predictive ability of pro-SFTPB. The area under the curve (AUC) values of the full model with and without pro-SFTPB were 0.741 (95% CI, 0.696 to 0.783) and 0.669 (95%CI, 0.620 to 0.717), respectively (difference in AUC, P_.001). Single markers are unlikely to have sufficient performance for implementation in a screening setting, hence the need to explore several discovery platforms to identify markers that provide complementary performance. Metabolomics represents a global unbiased approach to the profiling of small molecules and has been established as a platform for biomarker discovery for a variety of human biofluids and tissues. Here we used an untargeted liquid chromatography/mass spectrometry (MS) metabolomics approach to identify metabolites that distinguish human sera collected before the diagnosis of lung cancer from matched control sera in a prospective cohort of highrisk patients from the Beta-Carotene and Retinol Efficacy Trial (CARET).
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Long-term neural and physiological phenotyping of a single human
STUDY_TYPE
Longitudinal
STUDY_SUMMARY
The dynamics of human brain function are increasingly well understood at the short timescale of seconds/minutes (for example, through studies of learning) and the long timescale of years/decades (for example, through studies of development andageing), but almost nothing is known about how the human brainfunction varies across the range of days to months. This is a critical gap, because major psychiatric disorders show large fluctuations in brain function over this timescale. However, the kind of dense longitudinal phenotyping that is necessary to understand this question is extremely challenging with healthy human volunteers,who are unlikely to be sufficiently motivated to sustain frequent participation in a study over a long period. For this reason, the participation of motivated experimenters can be uniquely useful for demanding longitudinal studies. We investigated the long-range dynamics of brain function andtheir relation to a broad set of psychological and biological variables in a single healthy human (author R.A.P.) over the course of 532 days (along with several follow-up visits), representing one of the most intensive biological characterizations of a single individual ever performed (referred to hereafter as the MyConnectomestudy). The study was designed to measure the broadest possible range of human phenotypes (the phenome’3,4) to allow the widespread assessment of relations between psychological, neural and metabolic function. The results of the present study demonstrate that healthy brain function shows rich dynamics over the course of 18 months, and that these dynamics are paralleled by ongoing fluctuations in psychological and physiological function as observed in behaviour,gene expression and metabolomic measurements. These findings provide a proof of concept for the dynamic longitudinal phenotyping of individuals, which we propose will be crucial togain a better understanding of the substantial fluctuations in psychological and neural function in individuals with major psychiatric disorders.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
E.coli effects on growth and substrate uptake of green algae (part I - HILIC)
STUDY_SUMMARY
The purpose of this project was to quantify the exchange of thiamine between bacteria and algae. We previously observed that the model bacteria, Escherichia coli, enhanced the growth and substrate uptake of the green algae, Auxenochlorella protothecoides. We hypothesized that this growth enhancement was due to the secretion of thiamine derivatives or degradation products by E. coli followed by uptake of these compounds by A. protothecoides. Targeted and untargeted LCMS revealed the presence of thiamine dervatives in E. coli cell extracts. These LCMS methods were also used to quantify thiamine derivatives and two degradation products, HMP and THZ, present in E. coli medium after cell removal. The LCMS results along with culture studies were employed to show that thiamine derivatives and degradation products were the primary mechanism of symbiosis between E. coli and A. protothecoides.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
E.coli effects on growth and substrate uptake of green algae (part II - Reverse Phase)
STUDY_SUMMARY
The purpose of this project was to quantify the exchange of thiamine between bacteria and algae. We previously observed that the model bacteria, Escherichia coli, enhanced the growth and substrate uptake of the green algae, Auxenochlorella protothecoides. We hypothesized that this growth enhancement was due to the secretion of thiamine derivatives or degradation products by E. coli followed by uptake of these compounds by A. protothecoides. Targeted and untargeted LCMS revealed the presence of thiamine dervatives in E. coli cell extracts. These LCMS methods were also used to quantify thiamine derivatives and two degradation products, HMP and THZ, present in E. coli medium after cell removal. The LCMS results along with culture studies were employed to show that thiamine derivatives and degradation products were the primary mechanism of symbiosis between E. coli and A. protothecoides.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
Health Sciences Drive, Davis, California, 95616, USA
Inhibition of diamine oxidase promotes uptake of putrescine from rat small intestine
STUDY_SUMMARY
Metformin, a biguanide molecule, which is used as first line therapy for type 2 diabetes. In this study, we would like to investigate the inhibition of an enzyme called diamine oxidase (DAO) (also known as ABP1), by metformin. Based on our preliminary in vitro study using diamine oxidase enzyme, we saw increased level of putrescine with increasing metformin concentrations (see reference PMID: 26335661). This proposed in vivo study was to determine whether metformin could increase putrescine levels and other metabolites in mice. Aminoguanidine, a known inhibitor of DAO, in this study as positive control, following similar study design described in this paper (PMID: 8912017).
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Impact of glucose on the central metabolome of C. minutissima
STUDY_SUMMARY
Axenic Chlorella minutissima (UTEX 2341) was grown under mixotrophic and autotrophic conditions to compare metabolome differences. The purpose of this study was to understand how glucose impacted the central metabolome of C. minutissima.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
The proton channel HVCN1 is expressed in B cell malignancies at high levels but its role remains unclear. From initial experiments during which HVCN1 was downregulated in human multiple myeloma cell lines, we observed an increase in some glycolytic and TCA metabolites. We want to get a better idea if HVCN1 is playing a role in regulating energy metabolism in multiple myeloma.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Metabolomic Profiling in Early Pregnancy using Pre-Diagnostic Sera from Women Who Developed Placental Abruption
STUDY_TYPE
Metabolomics Biocrates Panel
STUDY_SUMMARY
Placental abruption (PA) is an ischemic placental disorder that results from the premature separation of the placenta from the wall of the uterus before delivery of the fetus. This disorder is associated with pre-term delivery, fetal death, maternal hemorrhagic shock, and renal failure. Several physiologic disturbances, such as oxidative stress, carbohydrate/fatty acid metabolism, and mitochondrial dysfunction, have been associated with ischemic placental disorder as well as with placental abruption. This preliminary study proposes to identify metabolites associated with incident placental abruption using existing serum and clinical data from a previously studied cohort. Metabolomics analysis will be carried out on maternal serum (51 cases and 51 controls) collected in early pregnancy (early second trimester).
INSTITUTE
Harvard School of Public Health
DEPARTMENT
Swedish Medical Center
LAST_NAME
Wlliams
FIRST_NAME
Michelle
ADDRESS
677 Huntington Ave. Kresge Room 905A, Boston, MA 02446
Metabolic profiling during ex vivo machine perfusion of the human liver
STUDY_SUMMARY
As donor organ shortages persist, functional machine perfusion is under investigation to improve preservation of the donor liver. The transplantation of donation after circulatory death (DCD) livers is limited by poor outcomes, but its application may be expanded by ex vivo repair and assessment of the organ before transplantation. Here we employed subnormothermic (21 °C) machine perfusion of discarded human livers combined with metabolomics to gain insight into metabolic recovery during machine perfusion. Improvements in energetic cofactors and redox shifts were observed, as well as reversal of ischemia-induced alterations in selected pathways, including lactate metabolism and increased TCA cycle intermediates. We next evaluated whether DCD livers with steatotic and severe ischemic injury could be discriminated from ‘transplantable’ DCD livers. Metabolomic profiling was able to cluster livers with similar metabolic patterns based on the degree of injury. Moreover, perfusion parameters combined with differences in metabolic factors suggest variable mechanisms that result in poor energy recovery in injured livers. We conclude that machine perfusion combined with metabolomics has significant potential as a clinical instrument for the assessment of preserved livers.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Metabolic profiling during ex vivo machine perfusion of the human liver (part III)
STUDY_SUMMARY
As donor organ shortages persist, functional machine perfusion is under investigation to improve preservation of the donor liver. The transplantation of donation after circulatory death (DCD) livers is limited by poor outcomes, but its application may be expanded by ex vivo repair and assessment of the organ before transplantation. Here we employed subnormothermic (21 °C) machine perfusion of discarded human livers combined with metabolomics to gain insight into metabolic recovery during machine perfusion. Improvements in energetic cofactors and redox shifts were observed, as well as reversal of ischemia-induced alterations in selected pathways, including lactate metabolism and increased TCA cycle intermediates. We next evaluated whether DCD livers with steatotic and severe ischemic injury could be discriminated from ‘transplantable’ DCD livers. Metabolomic profiling was able to cluster livers with similar metabolic patterns based on the degree of injury. Moreover, perfusion parameters combined with differences in metabolic factors suggest variable mechanisms that result in poor energy recovery in injured livers. We conclude that machine perfusion combined with metabolomics has significant potential as a clinical instrument for the assessment of preserved livers.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
The first 4 samples were a test run to see how efficient the analysis was and were run on a lipidomics platform. The next 12 samples were the used in the paper and were the same as the original 4 samples, but they were split into 3 biological replicates and run on the GC platform.
Toxicokinetics and Metabolomic Disrupting of the Flame Retardant Mixture Firemaster 550
STUDY_TYPE
Low Dose and High Dose Exposure to Firemaster (FM) 550
STUDY_SUMMARY
Pregnant lab rats (dams) were assigned to three groups: a control group, which was not exposed to Firemaster (FM) 550; a low-dose group, which ingested 100 µg of FM550 once daily throughout pregnancy; and a high-dose group, which ingested 1000 µg FM550 on the same schedule. The placentas were harvested immediately after birth, frozen on dry ice and pulverized in liquid nitrogen via mortar and pestle. The overall objective is to investigate the differences in the metabolic profiles of the placentas in each phenotypic group.
INSTITUTE
RTI International
DEPARTMENT
RCMRC
LAST_NAME
Sumner
FIRST_NAME
Susan
ADDRESS
3040 E Cornwallis Road, Research Triangle Park, NC 27709
Controlled Human Exposure to Particulate Matter (PM) and Gaseous Co-Pollutants
STUDY_TYPE
Exposome Evaluation
STUDY_SUMMARY
This study is designed to provide the environmental aspects to support both the acquisition of study samples and the advancement of environmental chemical speciation information and data analyis needed. The aims of the study are as follows:1)Do the metabolomics profiles appear to be impacted by exposure to PM and NO2+PM. 2)are the metabolomic profiles related to the PM and NO2+PM distinct 3)which features (chemical or physical) of the PM and NO2+PM have the most significant impact on the metabolomic profiles.
INSTITUTE
RTI International
DEPARTMENT
RCMRC
LAST_NAME
Sumner
FIRST_NAME
Susan
ADDRESS
3040 E Cornwallis Road, Research Triangle Park, NC, 27519, USA
The role of CFTR in the regulation of intrinsic defense mechanisms of exocrine secretions
STUDY_SUMMARY
This study was designed as a pilot to determine if the concentrations of selected ions in salivary gland secretions were influenced by the absence of CFTR on the apical surfaces of glandular cells and ductal epithelia. To this end, five cystic fibrosis children homozygous for Phe508 were to be recruited with their heterozygous non-CF mothers. For adaptation and development of the assays to a microtiter format, saliva samples were collected from non-CF control subjects initially to optimize the assays recognizing that the volumes for analyses would be small. The values obtained with these non-CF control samples were also compared to that of the homozygous and heterozygous CF subjects. As residual volume permits, these samples will be further analyzed for metabolic constituent profiles.
INSTITUTE
RTI International
DEPARTMENT
RCMRC
LAST_NAME
Sumner
FIRST_NAME
Susan
ADDRESS
3040 E Cornwallis Road, Research Triangle Park, NC 27709
Impact Of High Sugar Diet On L-Arginine Metabolism In The Lung
STUDY_SUMMARY
Asthma is a progressive inflammatory airways disease that leads to structural airway changes and debilitating symptoms in many severely affected adults. We need novel therapeutic agents that are affordable, can decrease the reliance on steroids, and can improve quality of life. This clinical and mechanistic study has the potential to impact treatment of a subset of adult severe asthmatics and to further our understanding of the mechanisms of L-arginine metabolism and NO biology in the airways of asthmatics. We will pursue a clinical trial in subjects not well controlled on standard drug therapy; this strategy will address whether L-arginine is efficacious in patients receiving standard of care medications. In studies using animal models, we and others have shown that interventions that augment NO levels, through either supplementation of L-arginine or inhibition of arginase, decrease allergic airway inflammation and hyperresponsiveness-the two hallmarks of asthma. Overall, we hypothesize that a responder subset of adult severe asthma patients will derive clinical benefit from supplemental L-arginine therapy and that these patients will have a lower exhaled NO concentrations (<20 ppb) and a higher NOS2/Arg1 mRNA and protein ratio in their airway epithelial cells than non-responders. We aim to: 1) test the hypothesis that uncontrolled, adult severe asthma patients with exhaled breath NO concentrations <20 ppb will have fewer asthma exacerbations over 3 months when treated with L-arginine compared to patients with FeNO > 25, 2) determine the mechanisms by which L-arginine affects the regulation of NOS and arginase enzymes in primary airway epithelial cell cultures from severe asthmatic subjects, and 3) test the hypothesis that inhaled nanoparticle carrier formulations of L-arginine will decrease airway inflammation, airway hyperresponsiveness, and airway fibrosis at lower doses than systemically administered L-arginine. The major impact of our study will be to identify the adult severe asthma cohort that will benefit from supplemental L-arginine therapy. Our ultimate goal is to develop novel therapeutic agents to treat adult severe asthma patients better. PUBLIC HEALTH RELEVANCE: Asthma is a progressive inflammatory airways disease that leads to structural airway changes and debilitating symptoms in many severely affected adults. This clinical study has the potential to improve the care of adult severe asthmatics and to further our understanding of the mechanisms of L-arginine metabolism and nitric oxide biology in the lung. If we demonstrate that L-arginine supplementation can decrease asthma attacks in a subset of severe asthmatics, it will have great implications for future research as well as for the daily lives of patients with asthma.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
ms3076 T1D poor glycemic control and control samples
STUDY_TYPE
Plasma metabolites in T1 diabetes
STUDY_SUMMARY
The objective of the study was to determine whether T1D with good glycemic control have persistent abnormalities of metabolites and pathways that exist in T1D with poor glycemic control.
Type 1 Diabetes good glycemic control and controls samples
STUDY_TYPE
Plasma metabolites in T1 diabetes
STUDY_SUMMARY
The objective of the study was to determine whether T1D with good glycemic control have persistent abnormalities of metabolites and pathways that exist in T1D with poor glycemic control.
Differences in mycoplasma growth due to different mediums
STUDY_SUMMARY
The object is to learn if there are variations in the lipid profiles of the three genomic variants (relative to one another) and if there are difference the lipid profiles due to growth in medium having different supplements. Mycoplasmas are eubacteria, but have only a single plasma membrane and no cell wall. They acquire FAs and cholesterol and other (perhaps many unknown) lipids from the medium which is complex and contains mammalian serum. Various mycoplasma species have been shown to contain a wide spectrum of bacterial lipids, but the composition is unknown for this mycoplasma species. We are particularly interested in ratios of membrane lipids among our strains, in part to gain clues about differences in metabolic pathways pertinent to membrane biogenesis; and to predict any underlying features that could relate to the extremely different modes of cell propagation observed among these genomic constructs.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Non targeted metabolomics of gastrocnemius tissue samples obtained from 20 month old (old) mice- Both Sham and after inducing lung injury
STUDY_TYPE
Non targeted metabolomic analysis
STUDY_SUMMARY
Introduction: Older patients are more likely to acquire and die from acute respiratory distress syndrome (ARDS) and muscle weakness may be more significant in older survivors. Recent data implicate muscle ring finger protein 1 (MuRF1) in lung injury-induced skeletal muscle atrophy in young mice and identify an alternative role for MuRF1 in cardiac metabolism regulation through inhibition of fatty acid oxidation. Objectives: To develop a model of lung injury-induced muscle wasting in old mice and to evaluate the skeletal muscle metabolomic profile of adult and old acute lung injury (ALI) mice. Methods: Young (2 month), adult (6 month) and old (20 month) male C57Bl6J mice underwent Sham (intratracheal H2O) or ALI [intratracheal E. coli lipopolysaccharide (i.t. LPS)] conditions and muscle functional testing. Metabolomic analysis on gastrocnemius muscle was performed using gas chromatography-mass spectrometry (GC-MS). Results: Old ALI mice had increased mortality and failed to recover skeletal muscle function compared to adult ALI mice. Muscle MuRF1 expression was increased in old ALI mice at day 3. Non-targeted muscle metabolomics revealed alterations in amino acid biosynthesis and fatty acid metabolism in old ALI mice. Targeted metabolomics of fatty acid intermediates (acyl-carnitines) and amino acids revealed a reduction in long chain acyl-carnitines in old ALI mice. Conclusion: This study demonstrates age-associated susceptibility to ALI-induced muscle wasting which parallels a metabolomic profile suggestive of altered muscle fatty acid metabolism. MuRF1 activation may contribute to both atrophy and impaired fatty acid oxidation, which may synergistically impair muscle function in old ALI mice.
INSTITUTE
University of North Carolina, Duke University
DEPARTMENT
UNC McAllister Heart Institute, Duke Molecular Physiology Institute
LABORATORY
Multiple Centers
LAST_NAME
Willis, Ilaiwy
FIRST_NAME
Monte, Amro
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
Non targeted metabolomics of gastrocnemius tissue samples obtained from 6 month old (adult) mice- Both Sham and after inducing lung injury
STUDY_TYPE
Non targeted metabolomic analysis
STUDY_SUMMARY
Introduction: Older patients are more likely to acquire and die from acute respiratory distress syndrome (ARDS) and muscle weakness may be more significant in older survivors. Recent data implicate muscle ring finger protein 1 (MuRF1) in lung injury-induced skeletal muscle atrophy in young mice and identify an alternative role for MuRF1 in cardiac metabolism regulation through inhibition of fatty acid oxidation. Objectives: To develop a model of lung injury-induced muscle wasting in old mice and to evaluate the skeletal muscle metabolomic profile of adult and old acute lung injury (ALI) mice. Methods: Young (2 month), adult (6 month) and old (20 month) male C57Bl6J mice underwent Sham (intratracheal H2O) or ALI [intratracheal E. coli lipopolysaccharide (i.t. LPS)] conditions and muscle functional testing. Metabolomic analysis on gastrocnemius muscle was performed using gas chromatography-mass spectrometry (GC-MS). Results: Old ALI mice had increased mortality and failed to recover skeletal muscle function compared to adult ALI mice. Muscle MuRF1 expression was increased in old ALI mice at day 3. Non-targeted muscle metabolomics revealed alterations in amino acid biosynthesis and fatty acid metabolism in old ALI mice. Targeted metabolomics of fatty acid intermediates (acyl-carnitines) and amino acids revealed a reduction in long chain acyl-carnitines in old ALI mice. Conclusion: This study demonstrates age-associated susceptibility to ALI-induced muscle wasting which parallels a metabolomic profile suggestive of altered muscle fatty acid metabolism. MuRF1 activation may contribute to both atrophy and impaired fatty acid oxidation, which may synergistically impair muscle function in old ALI mice.
INSTITUTE
University of North Carolina, Duke University
DEPARTMENT
UNC McAllister Heart Institute, Duke Molecular Physiology Institute
LABORATORY
Multiple Centers
LAST_NAME
Willis, Ilaiwy
FIRST_NAME
Monte, Amro
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
C2C12 stretch cessation models muscle atrophy and anaplerotic changes in metabolism
STUDY_TYPE
GC-MS non-targeted metabolomic profiling
STUDY_SUMMARY
Studies of skeletal muscle disuse either in patients on bed rest or experimentally in animals(immobilization) have demonstrated that decreased protein synthesis is common, with transient parallel increases in protein degradation. Muscle disuse atrophy involves a process of transition from slow to fast myosin fiber types 6 . A shift toward glycolysis, decreased capacity for fat oxidation, and substrate accumulation in atrophied muscles have been reported as has accommodation of the liver with an increased gluconeogenic capacity. Recent studies have modeled skeletal muscle disuse by using cyclic stretch of differentiated myotubes (C2C12), which mimics the loading pattern of mature skeletal muscle, followed by cessation of stretch.We utilized this model to determine the metabolic changes using non-targeted metabolomics analysis of the media. We identified increases in amino acids resulting from protein degradation (largely sarcomere) that occurs with muscle atrophy that are involved in feeding the Kreb’s cycle through anaplerosis. Specifically, we identified increased alanine/proline metabolism (significantly elevated proline, alanine, glutamine, and asparagine) and increased -ketoglutaric acid, the proposed Kreb’s cycle intermediate being fed by the alanine/proline metabolic anaplerotic mechanism. Additionally, several unique pathways not clearly delineated in previous studies of muscle unloading were seen, including: 1) elevated ethanolamine and elevated keto-acids (e.g. 2-ketoleucine and 2-keovaline) represent intermediates in the Ehlrich amino acid degradation pathway, which feeds into a metabolic pathway supplying acetyl-CoA and 2-hydroxybutyrate (also significantly increased); and 2) elevated guanine, an intermediate of purine metabolism, was seen at 12 hours unloading. Given the interest in targeting different aspects of the ubiquitin proteasome system to inhibit protein degradation, this C2C12 system may allow the identification of direct and indirect alterations in metabolism due to anaplerosis or through other yet to be identified mechanisms using a non-targeted metabolomics approach.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister Heart Institute
LABORATORY
Mutliple Centers
LAST_NAME
Ilaiwy, WIllis
FIRST_NAME
Amro, Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
Preconcentration of organic solutes in urine by bubble bursting
STUDY_TYPE
Sample preparation for MS analysis
STUDY_SUMMARY
The chemical sensitivity of urine metabolomics analysis is greatly compromised due to the large amounts of inorganic salts in urine (NaCl, KCl), which are detrimental to analytical instrumentation, e.g. chromatographic columns or mass spectrometers. Traditional desalting approaches applied to urine pretreatment suffer from the chemical losses, which reduce the information depth of analysis. We aimed to test a simple approach for the simultaneous preconcentration and desalting of organic solutes in urine based on the collection of induced bursting bubble aerosols above the surface of urine samples. Bursting bubbles were generated at ambient conditions by feeding gas through an air diffuser at the bottom of diluted (200 times in ultrapure water) urine solution (50-500 mL). Collected aerosols were analyzed by the direct-infusion electrospray ionization mass spectrometry (ESI-MS). The simultaneous preconcentration (ca. 6-12 fold) and desalting (ca. 6-10 fold) of organic solutes in urine was achieved by the bursting bubble sample pretreatment, which allowed ca. 3-times higher number of identified urine metabolites by high-resolution MS analysis. No notable chemical discrimination effects were observed. The increased degree of MS data clustering was demonstrated on the principal component analysis of data sets from the urine of healthy people and from the urine people with renal insufficiency. At least 10 times higher sensitivity of trace drug detection in urine was demonstrated for clenbuterol and salbutamol. Our results indicate the high versatility of bubble bursting as a simple pretreatment approach to enhance the chemical depth and sensitivity of urine analysis.
INSTITUTE
Research Center for Obstetrics, Gynecology and Perinatology
DEPARTMENT
Department of System Biology in Reproduction
LABORATORY
Laboratory for Proteomics and Metabolomics of Human Reproduction
Follicular fluid lipidomics reveals lipid alterations by LH addition during IVF cycles
STUDY_SUMMARY
Purpose Ovulation induction protocols are key components for performing assisted reproduction treatments successfully. The objective of the present study was to estimate how LH addition to controlled ovarian stimulation protocols may affect the follicular fluid lipid profile of women undergoing in vitro fertilization treatment. Methods We conducted the study using 28 self-paired samples, 14 per group. The patients received FSH during their first cycle of ovarian stimulation (FSH group). If treatment did not result in pregnancy, the same patients returned for a new cycle and received stimulus with the addition of LH to the previous protocol (Low-dose-LH group). Lipidomics analysis was performed by UPLC-MSE mass spectrometry. Potential lipid biomarkers were identified by the software Progenesis QI. Statistical analysis was performed using the SPSS 18.0 and MetaboAnalyst 2.0 software.
INSTITUTE
Universidade Federal de Sao Paulo
DEPARTMENT
Surgery
LABORATORY
Centro de Pesquisa em Urologia
LAST_NAME
Da Costa
FIRST_NAME
Livia
ADDRESS
Rua Embau 231 - Vila Clementino, Sao Paulo, Sao Paulo, 04039060, Brazil
EMAIL
liviadovale@hotmail.com
PHONE
551138074062
NUM_GROUPS
2
TOTAL_SUBJECTS
28
NUM_FEMALES
14
STUDY_COMMENTS
The groups consists of the same 14 women submitted to two different controlled ovarian stimulation protocols (FSH or LH group)
Heterologous expression and detection of Apratoxins in E. coli
STUDY_TYPE
Organic extraction of E coli cultures harboring apratoxin gene cluster
STUDY_SUMMARY
The apratoxin gene cluster was recovered from fosmid DNA library. The gene set responsible for the biosynthesis of the polyketide backbone was introduced in E. coli BAP strain and expressed at 30C for 24 hours. Two sets of control and experimental samples with culture broth pH adjusted at 8 and 12 respectively was extracted with ethyl acetate and dried.
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LAST_NAME
Kallifidas
FIRST_NAME
Dimitris
ADDRESS
Medical Sciences Building, Rm P5-26, 1600 SW Archer Rd., FL32610
This targeted metabolomic analysis was performed on plasma samples from 39 normal controls (n=18 men and 21 women) and 45 subjects ((n = 22 men and 23 women) who met diagnostic criteria for ME/CFS by Institute of Medicine, Canadian, and Fukuda criteria.
INSTITUTE
University of California, San Diego
DEPARTMENT
The Mitochondrial and Metabolic Disease Center
LAST_NAME
Naviaux
FIRST_NAME
Robert
ADDRESS
214 Dikinson Street, CTF-C102, San Diego, CA, 92103
EMAIL
maviaux@ucsd.edu
PHONE
619-993-2904
NUM_GROUPS
2 groups for men (control and CFS) and 2 groups for women (control and CFS)
The alpha-1A adrenergic receptor agonist A61603 reduces cardiac polyunsaturated fatty acid-Heart raw data
STUDY_TYPE
GC-MS non-targeted metabolomic profiling
STUDY_SUMMARY
Studies of skeletal muscle disuse either in patients on bed rest or experimentally in animals(immobilization) have demonstrated that decreased protein synthesis is common, with transient parallel increases in protein degradation. Muscle disuse atrophy involves a process of transition from slow to fast myosin fiber types 6 . A shift toward glycolysis, decreased capacity for fat oxidation, and substrate accumulation in atrophied muscles have been reported as has accommodation of the liver with an increased gluconeogenic capacity. Recent studies have modeled skeletal muscle disuse by using cyclic stretch of differentiated myotubes (C2C12), which mimics the loading pattern of mature skeletal muscle, followed by cessation of stretch.We utilized this model to determine the metabolic changes using non-targeted metabolomics analysis of the media. We identified increases in amino acids resulting from protein degradation (largely sarcomere) that occurs with muscle atrophy that are involved in feeding the Kreb’s cycle through anaplerosis. Specifically, we identified increased alanine/proline metabolism (significantly elevated proline, alanine, glutamine, and asparagine) and increased -ketoglutaric acid, the proposed Kreb’s cycle intermediate being fed by the alanine/proline metabolic anaplerotic mechanism. Additionally, several unique pathways not clearly delineated in previous studies of muscle unloading were seen, including: 1) elevated ethanolamine and elevated keto-acids (e.g. 2-ketoleucine and 2-keovaline) represent intermediates in the Ehlrich amino acid degradation pathway, which feeds into a metabolic pathway supplying acetyl-CoA and 2-hydroxybutyrate (also significantly increased); and 2) elevated guanine, an intermediate of purine metabolism, was seen at 12 hours unloading. Given the interest in targeting different aspects of the ubiquitin proteasome system to inhibit protein degradation, this C2C12 system may allow the identification of direct and indirect alterations in metabolism due to anaplerosis or through other yet to be identified mechanisms using a non-targeted metabolomics approach.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister Heart Institute
LABORATORY
Mutliple Centers
LAST_NAME
Ilaiwy, WIllis
FIRST_NAME
Amro, Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
The alpha-1A adrenergic receptor agonist A61603 reduces cardiac polyunsaturated fatty acid-Serum raw data
STUDY_TYPE
GC-MS non-targeted metabolomic profiling
STUDY_SUMMARY
Studies of skeletal muscle disuse either in patients on bed rest or experimentally in animals(immobilization) have demonstrated that decreased protein synthesis is common, with transient parallel increases in protein degradation. Muscle disuse atrophy involves a process of transition from slow to fast myosin fiber types 6 . A shift toward glycolysis, decreased capacity for fat oxidation, and substrate accumulation in atrophied muscles have been reported as has accommodation of the liver with an increased gluconeogenic capacity. Recent studies have modeled skeletal muscle disuse by using cyclic stretch of differentiated myotubes (C2C12), which mimics the loading pattern of mature skeletal muscle, followed by cessation of stretch.We utilized this model to determine the metabolic changes using non-targeted metabolomics analysis of the media. We identified increases in amino acids resulting from protein degradation (largely sarcomere) that occurs with muscle atrophy that are involved in feeding the Kreb’s cycle through anaplerosis. Specifically, we identified increased alanine/proline metabolism (significantly elevated proline, alanine, glutamine, and asparagine) and increased -ketoglutaric acid, the proposed Kreb’s cycle intermediate being fed by the alanine/proline metabolic anaplerotic mechanism. Additionally, several unique pathways not clearly delineated in previous studies of muscle unloading were seen, including: 1) elevated ethanolamine and elevated keto-acids (e.g. 2-ketoleucine and 2-keovaline) represent intermediates in the Ehlrich amino acid degradation pathway, which feeds into a metabolic pathway supplying acetyl-CoA and 2-hydroxybutyrate (also significantly increased); and 2) elevated guanine, an intermediate of purine metabolism, was seen at 12 hours unloading. Given the interest in targeting different aspects of the ubiquitin proteasome system to inhibit protein degradation, this C2C12 system may allow the identification of direct and indirect alterations in metabolism due to anaplerosis or through other yet to be identified mechanisms using a non-targeted metabolomics approach.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister Heart Institute
LABORATORY
Mutliple Centers
LAST_NAME
Ilaiwy, WIllis
FIRST_NAME
Amro, Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
Metabolic Adaptation of Staphylococcus aureus to Host Immunity
STUDY_TYPE
Metabolomics Analysis of Methicillin-Resistant Staphylococcus aureus (MRSA) to host immunity.
STUDY_SUMMARY
This project is intended to study the metabolic adaptation of Methicillin-Resistant Staphylococcus aureus (MRSA) to host immunity. Because of the nature of the samples RTI RCMRC worked with Dr. Anthony R. Richardson so that the samples would be extracted at the University of North Carolina at Chapel Hill under the condition that were optimized by RTI RCMRC for broad spectrum metabolomics analysis.
Metabolomic changes during active immunization with anti-METH vaccines.
STUDY_SUMMARY
A targeted metabolomics analysis was performed on serum samples from rats immunized with a methamphetamine-like hapten covalently bound to keyhole limpet hemocyanin (KLH) monomers, and controls. The subjects were approximately 300 g adult male Sprague Dawley rats. RTI International RCMRC received pre-immune serum from RI 11-03A (n=12) which is a matched control serum that was collected before starting immunizations, and week 17 bleeds from RI 11-03A (n=12), RI 11-03B (n=8), and RI 11-03C (n=12). The A-C nomenclature denotes A) complete antigen with adjuvant, B) complete antigen without adjuvant and C) only KLH carrier protein and adjuvant without a METH-like hapten. The rats’ serum samples were extracted and prepared for a combined flow injection (FIA) and LC-MS/MS assay (Biocrates AbsoluteIDQ® p180 kit). The Biocrates AbsoluteIDQ® p180 kit (Biocrates Life Sciences AG, Innsbruck, Austria) can quantitatively measure ~188 biologically relevant metabolites from five analyte groups (acylcarnitines, amino acids, biogenic amines, glycerophospho- and sphingolipids, and hexoses) on a triple quadrupole mass spectrometer.
Metabolomics of Mice Cohousing and Microbiota Transfer
STUDY_SUMMARY
The mice serum samples were extracted and prepared for a combined flow injection (FIA) and LC-MS/MS assay (Biocrates AbsoluteIDQ® p180 kit). The Biocrates AbsoluteIDQ® p180 kit (Biocrates Life Sciences AG, Innsbruck, Austria) can quantitatively measure ~188 biologically relevant metabolites from five analyte groups (acylcarnitines, amino acids, biogenic amines, glycerophospho- and sphingolipids, and hexoses) on a triple quadrupole mass spectrometer.
Uniquely Tumor-Selective Englerin A Profoundly Alters Lipid Metabolism in Renal Cell Carcinoma inducing ER-Stress and an Acute Inflammatory Response
STUDY_TYPE
Metabolomic effect of Englerin A on renal cell carcinoma
STUDY_SUMMARY
This targeted metabolomic analysis was performed on renal cell carcinoma A498 cells with or without anti-cancer drug Englerin treatment for 24 and 48 h.
INSTITUTE
University of California, San Diego
DEPARTMENT
Department of Pediatrics
LAST_NAME
Batova
FIRST_NAME
Ayse
ADDRESS
La Jolla, CA 92093
EMAIL
abatova@ucsd.edu
PHONE
619-543-1962
NUM_GROUPS
Two groups for 24 h treatment (control and Eglerin treatment) and two groups for 48 h treatment. Each has 4 replicates
Streptococcus mutans organic acids/amino acid profiles, effect of oxidative stress; pilot
STUDY_TYPE
Amino acid/organic acid profiles of wild-type and mutant strain in response to H2O2 treatment over time.
STUDY_SUMMARY
S. mutans UA159 and ΔspxA1 will be grown in BHI to OD600 = 0.4. Each culture will be split in to 4 samples. For the first sample, 3E10 cells will immediately be harvested by fast filtration, scraped off of membrane into ice-cold PBS, and pelleted by centrifugation. The remaining three samples will be treated with H2O2 to 0.5 mM, and the harvesting process repeated after 15, 30 and 60 minutes.
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LABORATORY
Lemos-Abranches
LAST_NAME
Hardin
FIRST_NAME
Emily
ADDRESS
1395 Center Drive, PO Box 100424, Gainesville, FL 32610
Enterococcus faecalis nucleotide profiles following mupirocin or decoyinine
STUDY_TYPE
Exposure to mupirocin or decoyinine
STUDY_SUMMARY
Triplicate samples of E. faecalis OG1RF will be grown in FMC-AUG to OD600 = 0.25. The cultures will be split and exposed to DMSO, mupirocin (0.01mg/mL) or decoyinine (0.1mg/mL) for 15 minutes. 6E9 cells will be harvested by fast filtration, scraped off of membrane into ice-cold PBS, and pelleted by centrifugation, and stored at -80C until shipment.
INSTITUTE
Univeristy of Florida
DEPARTMENT
SECIM
LABORATORY
Lemos-Abranches
LAST_NAME
Kajfasz
FIRST_NAME
Jessica
ADDRESS
1395 Center Drive, PO Box 100424 Gainesville, FL 32610
Comparison between wild-type and mutant strain, as well as providing varying cell count input for WT
STUDY_SUMMARY
E. faecalis OG1RF and rel/relQ will be grown in FMC-AUG to OD600 = 0.25. 3E10 cells will be harvested by fast filtration, scraped off of membrane into ice-cold PBS, and pelleted by centrifugation. This process will be repeated with OG1RF only to harvest 3E9 and 3E8 cells. A second OG1RF sample of 3E10 cells will be scraped into formic acid; only acid-soluble extract willl be sent for this sample.
INSTITUTE
Univeristy of Florida
DEPARTMENT
SECIM
LABORATORY
Lemos-Abranches
LAST_NAME
Kajfasz
FIRST_NAME
Jessica
ADDRESS
1395 Center Drive, PO Box 100424 Gainesville, FL 32610
Exahustive degradation of nucleotide triphosphates
STUDY_TYPE
Comparison of degradation kinetics
STUDY_SUMMARY
The degradation kinetics of nucleotide triphosphates (ATP, GTP, UTP and CTP) were evaluated under boiling ethanol extraction conditions (95°C) during 0 to 300 minutes.
INSTITUTE
University of Groningen
DEPARTMENT
Analytical Biochemistry
LAST_NAME
Bischoff
FIRST_NAME
Rainer
ADDRESS
Antonius Deusinglaan 1 (XB20), Building 3226, room 601, 9713 AV Groningen, The Netherlands
Effect of the chemical environment on the degradation of nucleotide triphosphates
STUDY_TYPE
Endpoint measurement
STUDY_SUMMARY
The influence of particular groups of compounds/metabolites, mainly comprising major central carbon metabolites including amino acids, organic acids, sugar phosphates, coenzymes, etc, on the degradation profiles of nucleotide triphosphates extracted under typical boiling ethanol conditions was evaluated.
INSTITUTE
University of Groningen
DEPARTMENT
Analytical Biochemistry
LAST_NAME
Bischoff
FIRST_NAME
Rainer
ADDRESS
Antonius Deusinglaan 1 (XB20), Building 3226, room 601, 9713 AV Groningen, The Netherlands
Amino Acid Quantifcation of obese patients on a 16 week caloric restriction from Plasma
STUDY_TYPE
timecourse, quantitative measurements of amino acid
STUDY_SUMMARY
Caloric restriction (CR) improves insulin sensitivity and reduces the incidence of diabetes in obese individuals. The underlying mechanisms whereby CR improves insulin sensitivity are not clear. We evaluated the effect of 16 weeks of CR on whole-body insulin sensitivity by pancreatic clamp before and after CR in 11 obese participants (BMI = 35 kg/m2) compared with 9 matched control subjects (BMI = 34 kg/m2). Compared with the control subjects, CR increased the glucose infusion rate needed to maintain euglycemia during hyperinsulinemia, indicating enhancement of peripheral insulin sensitivity. This improvement in insulin sensitivity was not accompanied by changes in skeletal muscle mitochondrial oxidative capacity or oxidant emissions, nor were there changes in skeletal muscle ceramide, diacylglycerol, or amino acid metabolite levels. However, CR lowered insulin-stimulated thioredoxin-interacting protein (TXNIP) levels and enhanced nonoxidative glucose disposal. These results support a role for TXNIP in mediating the improvement in peripheral insulin sensitivity after CR.
D2 Glucose Quantifcation of obese patients on a 16 week caloric restriction from plasma
STUDY_TYPE
timecourse
STUDY_SUMMARY
Caloric restriction (CR) improves insulin sensitivity and reduces the incidence of diabetes in obese individuals. The underlying mechanisms whereby CR improves insulin sensitivity are not clear. We evaluated the effect of 16 weeks of CR on whole-body insulin sensitivity by pancreatic clamp before and after CR in 11 obese participants (BMI = 35 kg/m2) compared with 9 matched control subjects (BMI = 34 kg/m2). Compared with the control subjects, CR increased the glucose infusion rate needed to maintain euglycemia during hyperinsulinemia, indicating enhancement of peripheral insulin sensitivity. This improvement in insulin sensitivity was not accompanied by changes in skeletal muscle mitochondrial oxidative capacity or oxidant emissions, nor were there changes in skeletal muscle ceramide, diacylglycerol, or amino acid metabolite levels. However, CR lowered insulin-stimulated thioredoxin-interacting protein (TXNIP) levels and enhanced nonoxidative glucose disposal. These results support a role for TXNIP in mediating the improvement in peripheral insulin sensitivity after CR.
Distinct signatures of dental plaque metabolic byproducts dictated by periodontal inflammatory status
STUDY_SUMMARY
Onset of chronic periodontitis is associated with an aberrant polymicrobial community, termed dysbiosis. Findings of a recent model of its etiology suggested that dysbiosis holds a conserved metabolic signature as an emergent property. The purpose of this study was to identify robust biomarkers for periodontal inflammation severity. Furthermore, we investigated disease-associated metabolic signatures of periodontal microbiota using a salivary metabolomics approach. Collection of whole saliva samples was performed before and after removal of supragingival plaque (debridement). Periodontal inflamed surface area (PISA) was employed as an indicator of periodontal inflammatory status. Based on multivariate analyses using pre-debridement salivary metabolomics data, we found that the metabolites associated with higher PISA included cadaverine and hydrocinnamate, while uric acid and ethanolamine were associated with lower PISA. Next, we focused on dental plaque metabolic byproducts by selecting significantly decreased salivary metabolites following debridement. Metabolite set enrichment analysis revealed that polyamine metabolism, arginine and proline metabolism, butyric acid metabolism, and lysine degradation were distinctive metabolic signatures of dental plaque in the high PISA group, which may have relevance to the metabolic signatures of disease-associated communities. Collectively, our findings identified potential biomarkers of periodontal inflammatory status, while they also provide insight into metabolic signatures of dysbiotic communities.
M-CMV-infected N. tabacum plants with six symptoms (vein clearing, mosaic, chlorosis, partial green recovery, complete green recovery and secondary mosaic) were analyzed by LC-MS & GC-MS. In addition, the pathogenesis biomarker might be found by this untargeted global metabolomic analysis.
The goal of this project is to analyze the metabolic pool distribution of cerebral metabolites in response to cocaine administration and withdrawal as compared to control
In this study, two independent large cohorts of mature dates exhibiting substantial diversity in origin, varieties and fruit processing conditions were measured by metabolomics techniques in order to identify major determinants of the fruit metabotype. Additional samples reflecting different stages of date fruit ripening process has been included for 10 different fruit varieties.
Metabolic changes to maternal rat liver tissue during and post-pregnancy
STUDY_SUMMARY
Assessing metabolic changes to maternal rat liver tissue during and post-pregnancy. Liver tissue was harvested post-mortem from rats or mice without pregnancy (Nulliparous - NP), time course during pregnancy in days (P2-4, P11-13m P18-20), lactation day 10 (LD10), in during involution of the liver (I2, I4, I6, I8, I10) and 4-weeks regression after preganancy (R4).
Assessing metabolic changes to maternal rat liver tissue during and post-pregnancy (part II)
STUDY_SUMMARY
Assessing metabolic changes to maternal rat liver tissue during and post-pregnancy. Liver tissue was harvested post-mortem from rats or mice without pregnancy (Nulliparous - NP), time course during pregnancy in days (P2-4, P11-13m P18-20), lactation day 10 (LD10), in during involution of the liver (I2, I4, I6, I8, I10) and 4-weeks regression after preganancy (R4).
Plasma metabolomics profiling for fish maturation in blunt snout bream
STUDY_TYPE
Metabolomics experiment
STUDY_SUMMARY
We investigated the comprehensive metabolic profiles of plasma among immature females, mature females ready to spawn, as well as already spawned breeders of blunt snout bream (Megalobrama amblycephala). The purpose of this study was to screen out potential biomarkers for sexual mature female M. amblycephala compared to immature female individuals and already spawned breeders. The three groups were set up in this study, including one year old immature females, 2 years old sexually mature females ready to spawning and successfully spawning females of M. amblycephala. The plasma samples were collected to investigate the comprehensive metabolic profiles through UPLC-MS/MS based metabolomics analysis method. According to multivariate and univariate statistical analysis, plasma metabolite profiles of three groups were obviously separated, and the plasma metabolite profiles of immature female M. amblycephala were much more different from mature females ready to spawn as well as already spawned breeders. The differential plasma metabolites from three hormone related pathways including GnRH signaling pathway, steroid hormone biosynthesis and steroid biosynthesis, were further analyzed. A total of 29 metabolites were identified as differential biomarkers associated with the female maturation status
INSTITUTE
Huazhong Agricultural University, Wuhan
DEPARTMENT
College of Fisheries
LABORATORY
Key Lab of Freshwater Animal Breeding, Ministry of Agriculture
Canine Diabetes - Preliminary Evaluation of Testing Methods
STUDY_TYPE
Single time point blood collection
STUDY_SUMMARY
Blood was collected from diabetic dogs and healthy control dogs. Diabetic dogs and control dogs were breed matched where possible. Timing of blood collection after a meal was matched as best as possible. Serum was frozen at -80C.
Triple Quadrupole Mass Spectrometer to measure low abundance isotope enrichment in individual muscle proteins
STUDY_TYPE
isotope encrichment and comparison of mass spectrometer platforms, timecourse
STUDY_SUMMARY
Stable isotope-labeled amino acids have long been used to measure the fractional synthesis rate of proteins, although the mass spectrometry platforms used for such analyses have changed throughout the years. More recently, tandem mass spectrometers such as triple quadrupoles have been accepted as the standard platform for enrichment measurement due to their sensitivity and the enhanced specificity offered by multiple reaction monitoring (MRM) experiments. The limit in the utility of such platforms for enrichment analysis occurs when measuring very low levels of enrichment from small amounts of sample, particularly proteins isolated from two-dimensional gel electrophoresis (2D-GE), where interference from contaminant ions impact the sensitivity of the measurement. We therefore applied a high resolution orbitrap mass spectrometer to the analysis of [ring-13C6]-phenylalanine enrichment in individual muscle proteins isolated with 2D-GE. Comparison of samples analyzed on both platforms revealed that the high resolution MS has significantly improved sensitivity relative to the triple quadrupole MS at very low-level enrichments due to its ability to resolve interferences in the m/z dimension.
Multi-omics based identification of specific biochemical changes associated with PfKelch13-mutant artemisinin resistant Plasmodium
STUDY_TYPE
Cell type comparison
STUDY_SUMMARY
Two clonaly artemisinin resistant parasitised red blood cells (trophozoite stage) were compared with artemsinin sensitive parasitised red blood cells by metabolomics analysis.
INSTITUTE
Monash Institute of Pharmaceutical Sciences, Monash University
DEPARTMENT
Drug Delivery, Disposition and Dynamics
LABORATORY
Creek lab
LAST_NAME
Creek
FIRST_NAME
Darren
ADDRESS
381 Royal Parade, Parkville, Melbourne, VIC3052, Australia
Inbred mice are used to investigate many aspects of human physiology, including susceptibility to disease and response to therapies. Despite increasing evidence that the composition and function of the murine intestinal microbiota can substantially influence a broad range of experimental outcomes, relatively little is known about microbiome dynamics within experimental mouse populations. We investigated changes in the intestinal microbiome between C57BL/6J mice spanning six generations (assessed at generations 1, 2, 3 and 6), following their introduction to a stringently controlled facility. Faecal microbiota composition and function were assessed by 16S rRNA gene amplicon sequencing and liquid chromatography mass spectrometry, respectively. Significant divergence of the intestinal microbiota between founder and second generation mice, as well as continuing inter-generational variance, was observed. Bacterial taxa whose relative abundance changed significantly included Akkermansia, Turicibacter and Bifidobacterium (p< 0.05), all of which are recognised as having the potential to substantially influence host physiology. Shifts in microbiota composition were mirrored by corresponding differences in the faecal metabolome (r=0.57, p=0.0001), with notable differences in levels of tryptophan pathway metabolites and amino acids, including glutamine, glutamate and aspartate. The magnitude of these changes in the intestinal microbiota and metabolome characteristics during acclimation were on a scale with those observed between populations housed in separate facilities, which differed in regards to husbandry, barrier conditions and dietary intake. The microbiome variance reported here has major implications for experimental reproducibility, and as a consequence, experimental design and the interpretation of research outcomes across as wide range of contexts.
INSTITUTE
South Australian Health and Medical Research Institute
DEPARTMENT
Infection and Immunity Theme
LAST_NAME
Rogers
FIRST_NAME
Geraint
ADDRESS
SAHMRI, North Terrace, Adelaide, SA 5000, Australia
Metabolomics marker of brown adipose tissue in men
STUDY_SUMMARY
Objective: We aimed to identify metabolites in serum that are associated with BAT volume and activity in men. Methods: We assessed 163 metabolites in fasted serum of a cohort of twenty two healthy lean men (age 24.1 (21.7 – 26.6) years, BMI 22.1 (20.5 – 23.4) kg/m2) who subsequently underwent a cold-induced [18F]FDG PET-CT scan to assess BAT volume and activity. In addition, we included three replication cohorts consisting of in total thirty-seven healthy lean men that were similar with respect to age and BMI compared to the discovery cohort.
The goal of this project is to analyze the metabolic pool distribution of cerebral metabolites in response to cocaine administration and withdrawal as compared to control
IROA feasibility project; plasticizers as obesogens in zebrafish
STUDY_TYPE
(1) IROA label (2) Zebrafish exposed to DEHP
STUDY_SUMMARY
Zebrafish were fed IROA labelled nematodes (smaple 1-4); In a second experiment, zebrafish larvae were exposed to DEHP, a chemical that is a suspected obesogen.
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LAST_NAME
Martyniuk
FIRST_NAME
Chris
ADDRESS
2187 Mowry Rd. Bldg 471
EMAIL
cmartyn@ufl.edu
PHONE
352-294-4636
NUM_GROUPS
2
TOTAL_SUBJECTS
20
STUDY_COMMENTS
Expt 2: Two groups (control) + DEHP-treated (n=10 larvae pools or biological replicates)
Plasma metabolomic profiling of diabetic nephropathy in the steptozotocin induced type-1 diabetes mouse model
STUDY_SUMMARY
This metabolomics study evaluated plasma from wild-type and meprin β knockout mice after induction of diabetes with streptozotocin or treatment with sodium citrate control to understand how these factors influence the metabotype.
INSTITUTE
RTI International
LAST_NAME
Sumner
FIRST_NAME
Susan
ADDRESS
3040 E. Cornwallis Road, Research Triangle Park, NC 27709
Urine metabolomic profiling of diabetic nephropathy in the steptozotocin induced type-1 diabetes mouse model.
STUDY_SUMMARY
This metabolomics study evaluated urine from wild-type and meprin β knockout mice after induction of diabetes with streptozotocin or treatment with sodium citrate control to understand how these factors influence the metabotype.
INSTITUTE
RTI International
LABORATORY
NIH Eastern Regional Comphrehensive Metabolomics Resource Core at UNC Chapel Hill (ERCMRC)
LAST_NAME
Sumner
FIRST_NAME
Susan
ADDRESS
3040 E. Cornwallis Road, Research Triangle Park, NC 27709
Metabolomics of immunoglobulin-producing cells in IgA nephropathy
STUDY_SUMMARY
IgA nephropathy (IgAN), the most common primary glomerulonephritis, is characterized by deposits of IgA-containing immune complexes in the kidney glomeruli, as first described by Berger and Hinglais in 1968. IgAN is a major cause of end-stage renal disease with its associated cardio-renal morbidity and mortality. Analyses of the IgA deposits revealed that the IgA is exclusively of the IgA1 subclass and that this IgA1 is aberrantly glycosylated, deficient in galactose in some O-glycans (Gd-IgA1). Patients with IgAN have elevated serum levels of Gd-IgA1 bound by anti-glycan autoantibodies in circulating immune complexes (CIC) that are fundamental in driving disease pathology in an autoimmune process. We have recently shown that elevated serum levels of Gd-IgA1 in patients with IgAN predict disease progression. Thus, understanding the mechanisms behind Gd-IgA1 production will improve future treatment options, as there is presently no disease-specific therapy. A total of 24 cell pellets (4 replicates from 6 cell lines) were analyzed by LCMS metabolomics. Immortalized immunoglobulin-producing cell lines were generated from peripheral-blood lymphocytes from patients with IgAN and healthy controls as described in Suzuki, H., Moldoveanu, Z., Hall, S., et al. IgA1-secreting cell lines from patients with IgA nephropathy produce aberrantly glycosylated IgA1. J Clin Invest. 2008, 118, 629-639.
INSTITUTE
RTI International
LABORATORY
NIH Eastern Regional Comphrehensive Metabolomics Resource Core at UNC Chapel Hill (ERCMRC)
LAST_NAME
Sumner
FIRST_NAME
Susan
ADDRESS
3040 E. Cornwallis Road, Research Triangle Park, NC 27709
Maize plants were grown under three different temperature regimes: 1) normal day / normal night; 2) hot day / normal night; 3) hot day / hot night. Kernels from developing ears were taken 14, 16, 18, 22, 26 and 40 days after pollination.
Association of hemodialysis patient plasma trace metals with response to erythropoiesis stimulating agents
STUDY_TYPE
Metallomics
STUDY_SUMMARY
EDTA-Plasma from 110 hemodialysis patients participating in an NIDDK funded study were analyzed by ICP-MS for the concentration of As, Cd, Co, Cr, Cu, Mn, Mo, Ni, Pb, Sb, Se, Sn, V, and Zn. Associations were determined between trace metals and gender, race, hemodialysis status, hemoglobin at the time of draw (Hgb), total ESA dose for the month the sample was collected (EPO), and erythropoietin resistance index determined over the 6 months of treatment leading up to sample collection (ERI)
INSTITUTE
RTI International
LABORATORY
NIH Eastern Regional Comprehensive Metabolomics Resource Core at UNC Chapel Hill (ERCMRC)
LAST_NAME
Sumner
FIRST_NAME
Susan
ADDRESS
3040 E. Cornwallis Road, Research Triangle Park, NC 27709, USA
Large Scale HILIC Profiling of the Effects of Curcumin Supplementation of Older Adults: Relation to Vascular Function
STUDY_SUMMARY
Perform large scale profiling HILIC metabolite analysis related to nitric oxide biology, oxidative stress and inflammation in plasma before and after 12 weeks of oral curcumin (2000 mg/d) or placebo (double-blind, randomized) in men and women aged 45-79 years who are free from clinical cardiovascular disease.
INSTITUTE
Mayo Clinic
LAST_NAME
Seals
FIRST_NAME
Douglas
ADDRESS
Department of Integrative Physiology University of Colorado Boulder, CO 80309
Metabolomic study on a schizophrenia and type 2 diabetes susceptibility gene
STUDY_SUMMARY
a comprehensive serum metabolomic analysis in healthy subjects with different genotypes of rs12742393 (n=49 for AA, AC, and CC, respectively) using gas chromatography–time-of-flight mass spectrometry and ultra-performance liquid chromatography quadruple time-of-flight mass spectrometry.
INSTITUTE
Shanghai Jiao Tong University Affiliated Sixth People’s Hospital
Metabolome analysis of the cecal contents of GF mice and GF mice colonized with dominant gut microbes present in the ceca of neonatal and adult mice
STUDY_SUMMARY
Metabolome profiles of GF or GF mice reconstituted with Esherichia coli (EC), Bacteroides acidifaciens (Bac), or Clostridia consortium (CL) were compared.
Experiment HuA: Metabolomics of plasma samples from humans infected with Plasmodium vivax strain.
STUDY_TYPE
Longitudinal study and treatment of multiple individuals with Chloroquine
STUDY_SUMMARY
Patients with vivax malaria were enrolled in this study from June 2011 to December 2012 at the Fundacão de Medicina Tropical Doutor Heitor Vieira Dourado (FMT-HVD), an infectious disease referral center located in Manaus, Western Brazilian Amazon. This study, which required a 42-day follow-up period, was approved by the FMT-HVD Institutional Review Board and the Brazilian National Ethics Committee (CONEP) (IRB approval #: CAAE: 12516713.8.0000.0005). All protocols and documentation were reviewed and sample shipments approved by the Emory IRB. Male and female patients were eligible for inclusion if aged 6 months to 60 years, bodyweight ?5 kg, presenting a blood parasite density from 250 to 100,000 parasites/microliter and axillary temperature ?37.5°C or history of fever in the last 48 hours. Exclusion criteria were: use of antimalarials in the previous 30 days, refusal to be followed up for 42 days and any clinical complication. Patients received supervised treatment with 25 mg/kg of chloroquine (CQ) phosphate over a 3-day period (10 mg/kg on day 0 and 7.5 mg/kg on days 1 and 2). Primaquine (0.5 mg/kg per day for 7 days) was prescribed at the end of the 42-day follow-up period. Patients who vomited the first dose within 30 minutes after drug ingestion were re-treated with the same dose. Patients were evaluated on days 0, 1, 2, 3, 7, 14, 28 and 42 and, if they felt ill, at any time during the study period. Blood smear readings, complete blood counts, and diagnostic polymerase chain reaction (PCR) amplifications were performed at all time points. Three aliquots of 100 µL of whole blood from the day of a recurrence were spotted onto filter paper for later analysis by high performance liquid chromatography (HPLC) to estimate the levels of CQ and desethylchloroquine (DCQ) as previously described. In this study, CQ-resistance with parasitological failure was defined as parasite recurrence in the presence of plasma concentrations of CQ and DSQ higher than 100 ng/mL and microsatellite analysis revealing the presence of the same clonal nature at diagnosis and recurrence. The CQ-sensitive control group consisted of patients with no parasitemia recurring during follow-up period. A group of 20 healthy individuals from Brazil was used as non-malarial control group. Within the MaHPIC, this project is known as ‘Experiment HuA’. This dataset was produced by Dean Jones at Emory University.
INSTITUTE
Emory University
DEPARTMENT
School of Medicine, Vaccine Center at Yerkes
LAST_NAME
Galinksi
FIRST_NAME
Mary
ADDRESS
Emory University, Yerkes National Primate Research Center, 954 Gatewood Rd, Room 003, Atlanta, GA 30329
AH and TM samples were obtained from young-normotensive DBA/2J (3 and 7.5 months) and old-hypertensive DBA/2J mice (8-8.5, 10 and 12 month). Lipids were extracted using modified Bligh and Dyer method and subjected to mass spectrometric identification using appropriate class-specific lipid standards and ratiometric quantification. Corresponding aqueous phase (of extraction) protein concentrations were measured using Bradford method.
INSTITUTE
University of Miami
LAST_NAME
Bhattacharya
FIRST_NAME
Sanjoy
ADDRESS
McKnight Vision Research Building, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Room 706A, Miami, Florida 33136
AH and TM samples were obtained from young-normotensive DBA/2J (3 and 7.5 months) and old-hypertensive DBA/2J mice (8-8.5, 10 and 12 month). Lipids were extracted using modified Bligh and Dyer method and subjected to mass spectrometric identification using appropriate class-specific lipid standards and ratiometric quantification. Corresponding aqueous phase (of extraction) protein concentrations were measured using Bradford method.
INSTITUTE
University of Miami
LAST_NAME
Bhattacharya
FIRST_NAME
Sanjoy
ADDRESS
McKnight Vision Research Building, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Room 706A, Miami, Florida 33136
The Metabolomics of Oral Biofilms exposed to Arginine and Fluoride
STUDY_SUMMARY
The study aims to use global metabolomics to investigate: (1) the metabolic profile of supragingival dental plaque from adults with different caries-status and from specific healthy and carious tooth-sites; and (2) the metabolic changes occurring in response to the use of the arginine or fluoride toothpastes for 12 weeks.
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LABORATORY
Nascimento/Garrett
LAST_NAME
Nascimento
FIRST_NAME
Marcelle
ADDRESS
1395 Center Drive, Room D9-6, PO Box 100415, Gainesville, FL 32610-0415
Fasting wildtype, tfeb -/- knockout, and lmna -/- knockout metabolite profiling of adult zebrafish
STUDY_SUMMARY
Inhibition of mechanistic target of rapamycin (mTOR) activity exerts cardioprotective functions. We propose to assess the metabolite profile in zebrafish cardiomyopathy models to test the cardioprotective role of mTOR-TFEB-autophagy and mTOR-lmna- autophagy signaling in heart, liver, muscle, brain, and kidney tissue. In addition mTOR signaling among zebrafish 2 hour post feeding, 24 hour post feeding, and 48 hour post feeding will be profiled. These studes will be used as a baseline and for protocol development before we assess changes in DOX-induced cardiomyopathy.
METABOLOMIC PROFILING OF FOLLICULAR FLUID FROM PATIENTS WITH INFERTILITY-RELATED DEEP ENDOMETRIOSIS.
STUDY_SUMMARY
the metaboloc qualitative profiling was performed by LC-MS in follicular fluid samples of controls and endometriosis patients undergoing in vitro fertilization treatment
Evaluation of specific concentrations for use in experimental protocol
STUDY_TYPE
GC-MS non-targeted metabolomic profiling
STUDY_SUMMARY
This study evaluated specific plasma concentrations and compared the optimal plasma extract volume established in the first study (Effects of dilution on analyte identification and quantification) with the volume previously used in the current institutional protocol. The findings of this study lead to recommendations for experimental design in GC-MS-based metabolomic profiling of human plasma.
Effects of dilution on analyte identification and quantification
STUDY_TYPE
GC-MS non-targeted metabolomic profiling
STUDY_SUMMARY
The limiting-dilution study evaluated the effects of sample dilution on the ability to identify and quantify analytes in plasma. The study was divided into 10 batches with identical experimental design spanning over a 16-day period. Each batch consisted of 33 aliquots with 11 different plasma extract volumes (0 – 700 µL) corresponding to 11 plasma concentrations repeated three times.
Metablomic profiling in acc1-5 mutant and wild type arabidiopsis
STUDY_SUMMARY
This experiment tests the metabolic consequence of a mutation at the ACC1 gene (At1g36160). The allele of acc1-5 bearing an EMS mutation, which cause a single amino acid substitution from aspartic acid to asparagine. Seedlings from both the acc1-5 mutant and the wild type were harvested and analyzed via HILIC LC-MS. Of particular interest are metabolites which would be affected by depletion of malonyl-CoA pools (flavenoids) and primary metabolites.
Experiment 13: Uninfected Macaca mulatta exposed to pyrimethamine to produce and integrate clinical, hematological, and omics control measures.
STUDY_SUMMARY
Uninfected, malaria-naive, male rhesus macaques (Macaca mulatta), approximately two years of age, were inoculated intravenously with a preparation of salivary gland material derived from non-infected Anopheles dirus and profiled for clinical, hematological, functional genomic, lipidomic, proteomic, and metabolomic measurements. Samples were generated and analyzed to investigate the effects of the pharmacological intervention with the anti-malarial drug pyrimethamine on normal individuals. The experiment was designed for 100 days plus a follow-up period, with pyrimethamine administered at three different time points to coincide with the predicted treatment days of experimentally infected rhesus macaques. Capillary blood samples were collected daily for the measurement of CBCs and reticulocytes. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood samples and bone marrow aspirates were collected at seven time points before and after three rounds of drug administration for functional genomic, proteomic, and lipidomic analyses. Within the MaHPIC, this project is known as 'Experiment 13'. This dataset was produced by Dean Jones at Emory University. The following contributed to the creation of this dataset: The MaHPIC Consortium, John Barnwell, Monica Cabrera, Jeremy D. DeBarry, Mary Galinski, Trenton Hoffman, Jay Humphrey, Jianlin Jiang, Chet Joyner, Nicolas Lackman, Stacey Lapp, Esmeralda Meyer, Alberto Moreno, Mustafa Nural, and Suman Pakala. The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC).
INSTITUTE
Emory University
DEPARTMENT
School of Medicine, Vaccine Center at Yerkes
LAST_NAME
Galinksi
FIRST_NAME
Mary
ADDRESS
Emory University, Yerkes National Primate Research Center, 954 Gatewood Rd, Room 003, Atlanta, GA 30329
EMAIL
mahpic@emory.edu
PHONE
none
TOTAL_SUBJECTS
6
STUDY_COMMENTS
31 samples, "The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC). These results are a product of a consortium of researchers known as the Malaria Host Pathogen Interaction Center (MaHPIC). For more information on the MaHPIC, please visit http://www.systemsbiology.emory.edu/ . Within the MaHPIC, these data were collected as part of 'Experiment 13' (E13). To access other publicly available results from E13 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp . This page will be updated as datasets are released to the public. See Pubmed ID:25453034 for the associated publication for this study."
PGD2 and other lipid mediator changes in mouse adipose associated with administration of an oral inhibitor of H-PGDS (HQL-79)
STUDY_SUMMARY
This is an additional experiment being added onto a previous mouse feeding study that aimed to identify changes in metabolites that occur in metabolic tissues in the obese state that are long-lasting and not reversed by weight loss. We observed in the previous mice feeding study that levels of PGD2 increased in HFD fed mice and stayed high after the diet switch. Other members of the Prostaglandin family followed a similar trend (15-deoxy PGJ2, PGJ2) and were specific to adipose tissue. Based on previously published data indicating that central injection of PGD2 stimulates food intake, we attempted to observe this effect using an oral PGD2 inhibitor of H-PGDS (HQL-79). In fact, the oral inhibitor of the H-PGDS (HQL-79) administered peripherally (oral gavage in mice at 30mg/kg dose) reduced daily food intake. Mice were divided into two groups termed Vehicle (Control) and HGL-79 (H-PGDS inhibitor). Each group was analyzed for lipid mediator changes (including PGD2) in adipose tissue by the Newman lab. Analytical results generally met quality control criterion with respect to surrogate recoveries and replicate precision. Surrogate recoveries were good for most oxylipins (58-76%), endocannabinoids (53-75%), and fatty acids (36%). Recovery precision was good for most analytes in these profiles, ranging from 6-28% RSD for most surrogates. The precision for the LTB4 surrogate was higher than most others (38%). Analytical precision was assessed by duplicate analysis of two separate study samples. Analytical precision was 62 - 69% of analytes having <30% RSD for all profiles and correlation analysis for the analytes within these samples ranged from 0.90-0.99 R2. The complete data set is in the associated excel file (Osborn HQL-79 – Deliverable Data Newman Lab.xls). There were few statistically significant differences observed when comparing concentrations (pmol/gr) between the control and HGL-79 treatment groups. However, when we compared ratios we saw numerous differences between PGD2 and its metabolite d15-PGJ2 versus other prostaglandins. Specifically, ratios between PGD2 and other connected pathway metabolites indicate a shift toward PGE2 and PGF2a production instead of PGD2 (Figure 1) with HQL-79 treatment. The PGD2 and PGE2 metabolites ratio of d15-PGJ2/15-keto PGE2 was statistically significant (P<0.01) using a two-tailed t-test. The ratios of PGD2/PGE2 and PGD2/PGF2 had p values of P<0.09 and P=0.07), respectively. Considering that we were predicting changes that indicated less PGD2 production it may be justifiable to use one-tailed tests instead. In order to maintain consistency with the metabolomic data analysis in the previous study, I followed the same statistical protocol that Johannes preformed for the main Pilot study. Using R and Devium log transformed data. Since this was a two group comparision, if the data was normal a 2 tailed t-test was used and if not normal then Mann-Whitney was used. A far as the significance of a shift from PGD2 to PGE2 production, I found a nice review article that discusses in detail the role of prostaglandins in white adipose tissue (Flachs et al. 2013). In the review it cites articles that have shown PGE2 to induce UCP1, modulate lipolysis adipogenesis, and stimulate leptin release. On the other hand, PGD2 was shown to increase adipogenesis and weight gain. Its downstream product d15-PGJ2 has been shown to increase adipogenesis, adipocyte differentiation, and decrease leptin production. This is significant since I also observed that the ratio of d15-PGJ2 to 15-keto PGE2 (the downstream product of PGE2) was also decreased. Another prostaglandin whose ratio versus PGD2 was different in the inhibitor group was PGF2a which has been shown to increase glucose transport in adipose tissue.
INSTITUTE
U.S.D.A. Western Human Nutrition Research Center, University of California, Davis
PGD2 and other lipid mediator changes in mouse adipose associated with administration of an oral inhibitor of H-PGDS (HQL-79)
STUDY_SUMMARY
This is an additional experiment being added onto a previous mouse feeding study that aimed to identify changes in metabolites that occur in metabolic tissues in the obese state that are long-lasting and not reversed by weight loss. We observed in the previous mice feeding study that levels of PGD2 increased in HFD fed mice and stayed high after the diet switch. Other members of the Prostaglandin family followed a similar trend (15-deoxy PGJ2, PGJ2) and were specific to adipose tissue. Based on previously published data indicating that central injection of PGD2 stimulates food intake, we attempted to observe this effect using an oral PGD2 inhibitor of H-PGDS (HQL-79). In fact, the oral inhibitor of the H-PGDS (HQL-79) administered peripherally (oral gavage in mice at 30mg/kg dose) reduced daily food intake. Mice were divided into two groups termed Vehicle (Control) and HGL-79 (H-PGDS inhibitor). Each group was analyzed for lipid mediator changes (including PGD2) in adipose tissue by the Newman lab. Analytical results generally met quality control criterion with respect to surrogate recoveries and replicate precision. Surrogate recoveries were good for most oxylipins (58-76%), endocannabinoids (53-75%), and fatty acids (36%). Recovery precision was good for most analytes in these profiles, ranging from 6-28% RSD for most surrogates. The precision for the LTB4 surrogate was higher than most others (38%). Analytical precision was assessed by duplicate analysis of two separate study samples. Analytical precision was 62 - 69% of analytes having <30% RSD for all profiles and correlation analysis for the analytes within these samples ranged from 0.90-0.99 R2. The complete data set is in the associated excel file (Osborn HQL-79 – Deliverable Data Newman Lab.xls). There were few statistically significant differences observed when comparing concentrations (pmol/gr) between the control and HGL-79 treatment groups. However, when we compared ratios we saw numerous differences between PGD2 and its metabolite d15-PGJ2 versus other prostaglandins. Specifically, ratios between PGD2 and other connected pathway metabolites indicate a shift toward PGE2 and PGF2a production instead of PGD2 (Figure 1) with HQL-79 treatment. The PGD2 and PGE2 metabolites ratio of d15-PGJ2/15-keto PGE2 was statistically significant (P<0.01) using a two-tailed t-test. The ratios of PGD2/PGE2 and PGD2/PGF2 had p values of P<0.09 and P=0.07), respectively. Considering that we were predicting changes that indicated less PGD2 production it may be justifiable to use one-tailed tests instead. In order to maintain consistency with the metabolomic data analysis in the previous study, I followed the same statistical protocol that Johannes preformed for the main Pilot study. Using R and Devium log transformed data. Since this was a two group comparision, if the data was normal a 2 tailed t-test was used and if not normal then Mann-Whitney was used. A far as the significance of a shift from PGD2 to PGE2 production, I found a nice review article that discusses in detail the role of prostaglandins in white adipose tissue (Flachs et al. 2013). In the review it cites articles that have shown PGE2 to induce UCP1, modulate lipolysis adipogenesis, and stimulate leptin release. On the other hand, PGD2 was shown to increase adipogenesis and weight gain. Its downstream product d15-PGJ2 has been shown to increase adipogenesis, adipocyte differentiation, and decrease leptin production. This is significant since I also observed that the ratio of d15-PGJ2 to 15-keto PGE2 (the downstream product of PGE2) was also decreased. Another prostaglandin whose ratio versus PGD2 was different in the inhibitor group was PGF2a which has been shown to increase glucose transport in adipose tissue.
INSTITUTE
U.S.D.A. Western Human Nutrition Research Center, University of California, Davis
Dysfunctional lipid metabolism underlies the effect of the perinatal DDT exposure on the development of metabolic syndrome
STUDY_SUMMARY
This study aims to identify changes in lipid mediators in the hypothalamus with triphenyl phosphate (TPP) exposure. UC Davis type 2 diabetes mellitus (UCD-T2DM) rats were treated with TPP (n=8 per group) or not treated (n=8 per group). Each group was analyzed for oxylipin, nitro lipids, endocannabinoid, and endocannabinoid-like monoacylglycerol and N-acylethanolamide changes to investigate alterations in lipid mediator signaling due to TPP exposure. Targeted metabolomic analysis of lipid mediators in rat hypothalamus samples was performed by the Newman lab.
INSTITUTE
U.S.D.A. Western Human Nutrition Research Center, University of California, Davis
Dysfunctional lipid metabolism underlies the effect of the perinatal DDT exposure on the development of metabolic syndrome
STUDY_SUMMARY
This study aims to identify changes in lipid mediators in the hypothalamus with triphenyl phosphate (TPP) exposure. UC Davis type 2 diabetes mellitus (UCD-T2DM) rats were treated with TPP (n=8 per group) or not treated (n=8 per group). Each group was analyzed for oxylipin, nitro lipids, endocannabinoid, and endocannabinoid-like monoacylglycerol and N-acylethanolamide changes to investigate alterations in lipid mediator signaling due to TPP exposure. Targeted metabolomic analysis of lipid mediators in rat hypothalamus samples was performed by the Newman lab.
INSTITUTE
U.S.D.A. Western Human Nutrition Research Center, University of California, Davis
Metabolomics measures of Macaca mulatta infected with Plasmodium coatneyi Hackeri strain to produce and integrate clinical, hematological, parasitological, and omics measures of acute, recrudescent, and chronic infections.
STUDY_TYPE
Longitudinal parasite infection and treatment of multiple individuals
STUDY_SUMMARY
Malaria-naive male rhesus macaques (Macaca mulatta), approximately four years of age, were inoculated intravenously with salivary gland sporozoites produced and isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment was designed for 100 days, and pre- and post-100 day periods to prepare subjects and administer curative treatments respectively. The anti-malarial drug artemether was subcuratively administered to all subjects at the initial peak of infection, one out of the five macaques received four additional subcurative treatments for subsequent recrudescence peaks. The experimental infection in one subject was ineffective but the macaque was followed-up for the same period of 100 days. The different clinical phases of the infection were clinically determined for each subject. Blood-stage curative doses of artemether were administered to all subjects at the end of the study. Capillary blood samples were collected daily for the measurement of CBCs, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood and bone marrow samples were collected at seven time points for functional genomic, proteomic, lipidomic, and immunological analyses. Within the MaHPIC, this project is known as ‘Experiment 03’. This dataset was produced by Dean Jones at Emory University. The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC).
INSTITUTE
Emory University
DEPARTMENT
School of Medicine, Vaccine Center at Yerkes
LAST_NAME
Galinski
FIRST_NAME
Mary
ADDRESS
Emory University, Yerkes National Primate Research Center, 954 Gatewood Rd, Room 003, Atlanta, GA 30329
EMAIL
mahpic@emory.edu
PHONE
N/A
NUM_GROUPS
6
TOTAL_SUBJECTS
331
STUDY_COMMENTS
The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC). These results are a product of a consortium of researchers known as the Malaria Host Pathogen Interaction Center (MaHPIC). Contributors include: Monica Cabrera, Jeremy D. DeBarry, Mary G. Galinski, Jay Humphrey, Dean Jones, Ebru Karpuzoglu, Jessica C. Kissinger, Regina Joice, Esmeralda Meyer, Vishal Nayak, Mustafa Nural, Suman Pakala, ViLinh Tran, Karan Uppal, Loukia Williams. For more information on the MaHPIC, please visit http://www.systemsbiology.emory.edu/ . Within the MaHPIC, these data were collected as part of 'Experiment 03' (E03). To access other publicly available results from E03 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp . This page will be updated as datasets are released to the public.
NEFA Profile Response to Triphenyl Phosphate Exposure
STUDY_SUMMARY
This study aims to identify changes in non-esterified fatty acid (NEFAs) in the plasma with triphenyl phosphate (TPP) exposure. UC Davis type 2 diabetes mellitus (UCD-T2DM) rats were treated with TPP or not treated. Each group was analyzed for non-esterified fatty acid (NEFA) changes to investigate alterations in NEFAs due to TPP exposure. Targeted analysis of NEFA in rat plasma samples was performed by the Newman lab.
INSTITUTE
U.S.D.A. Western Human Nutrition Research Center, University of California, Davis
DEPARTMENT
Nutrition
LAST_NAME
Newman
FIRST_NAME
John
ADDRESS
430 W. Health Sciences Dr., Davis, CA 95616
EMAIL
john.newman@ars.usda.gov
PHONE
+1-530-752-1009
STUDY_COMMENTS
The samples included a high degree of hemolysis exhibited in the plasma. One sample was lost during processing (Group E- Subject 78). Two samples were outliers for multiple analytes and were not included in the final data (E-117 & T-28). Of the samples reported in this data set, there were no missing values.
Untargeted LC-MS metabolomics analysis of human COPD plasma, HILIC & C18
STUDY_SUMMARY
Identify perturbed metabolites and pathways in human plasma collected from 131 COPD subjects. Subjects were either current or former smokers with various COPD phenotypes including emphysema, and exacerbations.
Urinary Volatile Compound, Associated with Chronic Inflammation In Interstitial Cystitis
STUDY_SUMMARY
Interstitial cystitis (IC)/bladder pain syndrome (BPS) is a clinical condition that manifests as a sensory hypersensitivity of unknown cause and is characterized by urinary frequency, bladder discomfort, and pelvic pain. In the present volatolomic study, we have analyzed the VOCs unique to urine specimens obtained from interstitial cystitis patients, in compassion to healthy controls.This is the novel finding from comprehensive and unbiased metabolomics analysis that urinary menthol is decreased in urine specimens from IC patients, and that the reduced menthol level in IC is potentially linked to the chronic inflammation, which is often observed in IC patients
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
Health Sciences Drive, Davis, California, 95616, USA
Impact Of High Sugar Diet On L-Arginine Metabolism In The Lung
STUDY_SUMMARY
Asthma is a progressive inflammatory airways disease that leads to structural airway changes and debilitating symptoms in many severely affected adults. We need novel therapeutic agents that are affordable, can decrease the reliance on steroids, and can improve quality of life. This clinical and mechanistic study has the potential to impact treatment of a subset of adult severe asthmatics and to further our understanding of the mechanisms of L-arginine metabolism and NO biology in the airways of asthmatics. We will pursue a clinical trial in subjects not well controlled on standard drug therapy; this strategy will address whether L-arginine is efficacious in patients receiving standard of care medications. In studies using animal models, we and others have shown that interventions that augment NO levels, through either supplementation of L-arginine or inhibition of arginase, decrease allergic airway inflammation and hyperresponsiveness-the two hallmarks of asthma. Overall, we hypothesize that a responder subset of adult severe asthma patients will derive clinical benefit from supplemental L-arginine therapy and that these patients will have a lower exhaled NO concentrations (<20 ppb) and a higher NOS2/Arg1 mRNA and protein ratio in their airway epithelial cells than non-responders. We aim to: 1) test the hypothesis that uncontrolled, adult severe asthma patients with exhaled breath NO concentrations <20 ppb will have fewer asthma exacerbations over 3 months when treated with L-arginine compared to patients with FeNO > 25, 2) determine the mechanisms by which L-arginine affects the regulation of NOS and arginase enzymes in primary airway epithelial cell cultures from severe asthmatic subjects, and 3) test the hypothesis that inhaled nanoparticle carrier formulations of L-arginine will decrease airway inflammation, airway hyperresponsiveness, and airway fibrosis at lower doses than systemically administered L-arginine. The major impact of our study will be to identify the adult severe asthma cohort that will benefit from supplemental L-arginine therapy. Our ultimate goal is to develop novel therapeutic agents to treat adult severe asthma patients better. PUBLIC HEALTH RELEVANCE: Asthma is a progressive inflammatory airways disease that leads to structural airway changes and debilitating symptoms in many severely affected adults. This clinical study has the potential to improve the care of adult severe asthmatics and to further our understanding of the mechanisms of L-arginine metabolism and nitric oxide biology in the lung. If we demonstrate that L-arginine supplementation can decrease asthma attacks in a subset of severe asthmatics, it will have great implications for future research as well as for the daily lives of patients with asthma.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Comparing identified and statistically significant lipids and polar metabolites in 15-year old serum and dried blood spot samples for longitudinal studies
STUDY_SUMMARY
The use of dried blood spots (DBS) has many advantages over traditional plasma and serum samples such as the smaller blood volume required, storage at room temperature, and ability to sample in remote locations. However, understanding the robustness of different analytes in DBS samples is essential, especially in older samples collected for longitudinal studies. Here we analyzed the stability of polar metabolites and lipids in DBS samples collected in 2000-2001 and stored at room temperature. The identified and statistically significant molecules were then compared to matched serum samples stored at –80°C to determine if the DBS samples could be effectively used in a longitudinal study following metabolic disease. A total of 400 polar metabolites and lipids were identified in the serum and DBS samples using gas chromatograph/mass spectrometry (GC/MS), liquid chromatography (LC)/MS, and LC/ion mobility spectrometry-MS (LC/IMS-MS). The identified polar metabolites overlapped well between the sample types, though only one statistically significant metabolite was conserved in a case-control study of older diabetic males with low amounts of high-density lipoproteins and high body mass indices, triacylglycerides and glucose levels when compared to non-diabetic patients with normal levels, indicating that degradation in the DBS samples affects polar metabolite quantitation. Differences in the lipid identifications indicated that some oxidation occurs in the DBS samples. However, 36 statistically significant lipids correlated in both sample types. The difference in the number of statistically significant polar metabolites and lipids indicated that the lipids did not degrade to as great of a degree as the polar metabolites in the DBS samples and lipid quantitation was still possible.
LC/MS-MS measurement of inosine to adenosine ratio as well as GC/MS measurement of sarcosine relative values in urine samples from prostate cancer and case control patients in a group of ancestry verified African American and European American.
Sphingolipid Analysis of Human Aqueous Humor in Glaucomatous and Control eyes
STUDY_SUMMARY
This study examined the profiles of sphin¬golipids and ceramides present in the aqueous humor (AH) of human control and POAG donors. Furthermore, we quantitatively compared distinct differences between glaucomatous and age-matched control eyes, identifying potential molecules for further experimentation to determine their biological role in modulating cell behavior. Lipids were identified and ratiometrically quantified in a two-step process using precursor ion scan (PIS) or neutral loss scan (NLS) with appropriate class-specific lipid standards on a TSQ Quantum Access Max mass spectrometer following established procedures. We identified several species of sphingomyelin, sphingoid base, sphingoid base-1-phosphate, and ceramides that were common between control and glaucomatous AQH. Some unique lipid species in these classes were also identified in controls but not in glaucoma and vice versa.
We determined the profiles of sphingomyelin, sphingoid base, sphingoid base-1-phosphate, and ceramide, and their quantitative differences between control and glaucomatous trabecular meshwork (TM) derived from human donors.
INSTITUTE
University of Miami
LAST_NAME
Bhattacharya
FIRST_NAME
Sanjoy
ADDRESS
McKnight Vision Research Building, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Room 706A, Miami, Florida 33136
GC/MS measurement of sarcosine in urine samples from prostate cancer and case control patients in a group of ancestry verified African American and European Americans.
Human Aqueous Humor Phospholipids in Control and Glaucomatous eyes
STUDY_SUMMARY
An analysis of phospholipid (phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine and phosphatidylinositol) classes in human control and glaucomatous aqueous humor (AH). Lipid extraction was performed using a modification of the Bligh and Dyer method, protein concentrations were determined using the Bradford’s method, and select samples were confirmed with Densitometry of PHAST gels. Lipids were identified and subjected to ratiometric quantification using a TSQ Quantum Access Max triple quadrupole mass spectrometer utilizing precursor ion scan (PIS) or neutral ion loss scan (NLS) using appropriate class specific lipid standards in a two-step quantification process. Mass spectrometer data were analyzed using MzMine 2.23.
Validation of the application of targeted metabolomic appraoch in the diagnosis of CFS
STUDY_TYPE
Plasma metabolomic profiling
STUDY_SUMMARY
This study was to validate the utility of the developed targeted metabolomic method in the diagnosis of chronic fatigue syndrome (CFS). Clinical validation consisted of a cohort of 20 male CFS (53 ± 2.8 years old, mean ± SEM, range 21-67 y) and 18 male controls (53 ± 3.5 years old, mean ± SEM, range 23-69 y), who were enrolled in a previous study (Naviaux et al. 2016). These plasma samples were stored in -80 ºC for about 1.5 years and reanalyzed on a different LC-MS/MS system by a different investigator.
INSTITUTE
University of California, San Diego
DEPARTMENT
Department of Medicine
LABORATORY
The Mitochondrial and Metabolic Disease Center
LAST_NAME
Naviaux
FIRST_NAME
Robert
ADDRESS
214 Dikinson Street, CTF-C102, San Diego, CA, 92103
EMAIL
rnaviaux@ucsd.edu
PHONE
619-993-2904
NUM_GROUPS
2
TOTAL_SUBJECTS
38
NUM_MALES
38
STUDY_COMMENTS
These plasma samples were stored in -80 ºC for about 1.5 years and reanalyzed on a different LC-MS/MS system by a different investigator.
Metabolomic Profiling of Follicular Fluid from Patients with Polycystic Ovary Syndrome and Hyper Response to In Vitro Fertilization Treatment
STUDY_TYPE
MS quallitative analysis
STUDY_SUMMARY
The present study consisted in a metabolomic approach in follicular fluid samples from patients with polycystic ovary syndrome and hyper response to in vitro fertilization treatment.
INSTITUTE
Sao Paulo Federal University
DEPARTMENT
Department of Surgery, Division of Urology, Human Reproduction Section
Sphingolipid Analysis of hyper and normotensive DBA2J mice aqueous humor and trabecular meshwork
STUDY_SUMMARY
To determine the differential profiles of sphingomyelin, sphingoid base, sphingoid base-1-phosphate, and ceramide and their quantitative differences between trabecular meshwork (TM) and aqueous humor (AH) derived from normotensive and hypertensive intraocular pressure states of DBA/2J mice.
INSTITUTE
University of Miami
LAST_NAME
Bhattacharya
FIRST_NAME
Sanjoy
ADDRESS
McKnight Vision Research Building, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Room 706A, Miami, Florida 33136
Untargeted metabolomic changes in Chlamydomonas reinhardtii treated with lipid inducing small molecules
STUDY_SUMMARY
A study to investigate the effect of small molecule lipid inducing compounds that leads to hyper accumulation of lipids in N replete cells of Chlamydomonas reinhardtii. These compounds were identified through a high throughput screening designed for that purpose. During that screening, we screened 43,783 compounds and identified 367 primary hits. These 367 hits were further retested using a 8-point dilution series (from 0.25 to 30 uM) and verified the activity of 250 compounds that induce the hyper lipid accumulating phenotype in algae. Once the hit compounds were identified and confirmed, we then performed extensive chemoinformatics analysis to look for common scaffolds and identified several common substructures. We then selected 15 top performing compounds from 5 diverse structural groups and tested biochemical parameters such as growth, lipid accumulating capacity, effect on photosynthetic rates, respiration rates, oxygen consumption rates, analysis of different lipid species to quantify and identify fatty acid species using GC-MS. To understand the global changes in the metabolome, 2 structurally different compounds were selected and compared with cells grown without compounds as control for untargeted metabolomics analysis.
Identification and metabolite profiling of chemical activators of lipid accumulation in green algae
STUDY_TYPE
GC-MS metabolite profiling of algal lipid activators
STUDY_SUMMARY
Microalgae are proposed as feedstock organisms useful for producing biofuels and co-products. However, several limitations must be overcome before algae-based production is economically feasible. Among these is the ability to induce lipid accumulation and storage without affecting biomass yield. To overcome this barrier, a chemical genetics approach was employed in which 43,783 compounds were screened against Chlamydomonas reinhardtii and 243 compounds were identified that increase triacylglyceride (TAG) accumulation without terminating growth. Identified compounds were classified by structural similarity and 15 selected for secondary analyses addressing impacts on growth fitness, photosynthetic pigments, and total cellular protein and starch concentrations. TAG accumulation was verified using GC-MS quantification of total fatty acids and targeted TAG and galactolipid (GL) measurements using LC-MRM/MS. These results demonstrated TAG accumulation does not necessarily proceed at the expense of GL. Untargeted metabolite profiling provided important insights into pathway shifts due to 5 different compound treatments and verified the anabolic state of the cells with regard to the oxidative pentose phosphate pathway, Calvin cycle, tricarboxylic acid cycle and amino acid biosynthetic pathways. Metabolite patterns were distinct from nitrogen starvation and other abiotic stresses commonly used to induce oil accumulation in algae. The efficacy of these compounds was also demonstrated in 3 other algal species. These lipid inducing compounds offer a valuable set of tools for delving into the biochemical mechanisms of lipid accumulation in algae and a direct means to improve algal oil content independent of the severe growth limitations associated with nutrient deprivation.
INSTITUTE
Univ of Nebraska-Lincoln
DEPARTMENT
Biochemistry
LABORATORY
FATTTLab
LAST_NAME
Wase
FIRST_NAME
Nishikant
ADDRESS
1901 Beadle Center, Vine Street, 1901 VINE STREET, Lincoln, NE, 68588-0664, USA
Non targeted metabolomic analysis of mouse and human bronchoalveolar lavage fluid, Aqueous(+) experiment (part I)
STUDY_TYPE
Comprehensive profile
STUDY_SUMMARY
Mouse BALF was collected from C57BL/6 mice (n = 10). Five mice were exposed to ambient air for one day (air control) and five mice were exposed to CS for nine months (smoking). Human BALF was collected from subjects from the COPDGene cohort (n = 5). COPD diagnosis was based on the ratio of forced expiratory volume in 1 second to forced vital capacity (FEV1/FVC). Subjects were 45-70 years old, BMI 27-45, weight 76-125kg, and were categorized as follows: 1 male former smoker without COPD (FEV1/FVC = 0.82), 2 male current smokers without COPD (FEV1/FVC = 0.91 and 0.79), 1 female current smoker with moderate COPD (FEV1/FVC = 0.51), and 1 male current smoker with moderate COPD (FEV1/FVC = 0.64).
Non targeted metabolomic analysis of mouse and human bronchoalveolar lavage fluid, Lipid(-) experiment
STUDY_TYPE
Comprehensive profile
STUDY_SUMMARY
Mouse BALF was collected from C57BL/6 mice (n = 10). Five mice were exposed to ambient air for one day (air control) and five mice were exposed to CS for nine months (smoking). Human BALF was collected from subjects from the COPDGene cohort (n = 5). COPD diagnosis was based on the ratio of forced expiratory volume in 1 second to forced vital capacity (FEV1/FVC). Subjects were 45-70 years old, BMI 27-45, weight 76-125kg, and were categorized as follows: 1 male former smoker without COPD (FEV1/FVC = 0.82), 2 male current smokers without COPD (FEV1/FVC = 0.91 and 0.79), 1 female current smoker with moderate COPD (FEV1/FVC = 0.51), and 1 male current smoker with moderate COPD (FEV1/FVC = 0.64)
Effects of NO Donor Therapy on the Dystrophic Mouse Heart Metabolome (part VII)
STUDY_SUMMARY
For this aim, we will only use male mdx mice. We will study three groups treated for 7 days with vehicle, naproxcinod (i.e., NO-naproxen), or naproxen (n = 10 each group). Two hours after the final treatment, half the mice in each group will be run to exhaustion on a treadmill. The heart and gastrocnemius, soleus, and quadriceps muscles of one hindlimb will be sent to the Mayo Clinic Metabolomics Resource Core. The heart and quadriceps muscle will be used for untargeted metabolomics profiling (LC/MS).
INSTITUTE
Mayo Clinic
LAST_NAME
Thomas
FIRST_NAME
Gail
ADDRESS
Penn State Hershey Heart and Vascular Institute Penn State College of Medicine 500 University Drive, MC H047 Hershey, PA 17033
Effects of NO Donor Therapy on the Dystrophic Mouse Quadricep Metabolome (part VIII)
STUDY_SUMMARY
For this aim, we will only use male mdx mice. We will study three groups treated for 7 days with vehicle, naproxcinod (i.e., NO-naproxen), or naproxen (n = 10 each group). Two hours after the final treatment, half the mice in each group will be run to exhaustion on a treadmill. The heart and gastrocnemius, soleus, and quadriceps muscles of one hindlimb will be sent to the Mayo Clinic Metabolomics Resource Core. The heart and quadriceps muscle will be used for untargeted metabolomics profiling (LC/MS).
INSTITUTE
Mayo Clinic
LAST_NAME
Thomas
FIRST_NAME
Gail
ADDRESS
Penn State Hershey Heart and Vascular Institute Penn State College of Medicine 500 University Drive, MC H047 Hershey, PA 17033
Effects of Exercise on Dystrophic Mouse Heart Meabolome (part IX)
STUDY_SUMMARY
We will use male C57BL10, mdx, and nNOS-/- mice (n = 10 each group) to characterize the skeletal and cardiac muscle metabolomes. Half of the mice in each group will remain sedentary while the other half will be subjected to a single bout of treadmill exercise to exhaustion. Mice will be euthanized immediately postexercise and blood, hearts, and hindlimb muscles will be harvested and frozen as detailed in the General Methods. The heart and gastrocnemius, soleus, and quadriceps muscles of one hindlimb will be sent to the Mayo Clinic Metabolomics Resource Core. The heart and quadriceps muscle will be used for untargeted metabolomics profiling (LC/MS) while the gastrocnemius and soleus muscles will be used for targeted analyses of amino acids plus amino metabolites, non-esterified fatty acids, and citric acid cycle intermediates.
INSTITUTE
Mayo Clinic
LAST_NAME
Thomas
FIRST_NAME
Gail
ADDRESS
Penn State Hershey Heart and Vascular Institute Penn State College of Medicine 500 University Drive, MC H047 Hershey, PA 17033
Effects of Exercise on Dystrophic Mouse Quadricep Meabolome (part X)
STUDY_SUMMARY
We will use male C57BL10, mdx, and nNOS-/- mice (n = 10 each group) to characterize the skeletal and cardiac muscle metabolomes. Half of the mice in each group will remain sedentary while the other half will be subjected to a single bout of treadmill exercise to exhaustion. Mice will be euthanized immediately postexercise and blood, hearts, and hindlimb muscles will be harvested and frozen as detailed in the General Methods. The heart and gastrocnemius, soleus, and quadriceps muscles of one hindlimb will be sent to the Mayo Clinic Metabolomics Resource Core. The heart and quadriceps muscle will be used for untargeted metabolomics profiling (LC/MS) while the gastrocnemius and soleus muscles will be used for targeted analyses of amino acids plus amino metabolites, non-esterified fatty acids, and citric acid cycle intermediates.
INSTITUTE
Mayo Clinic
LAST_NAME
Thomas
FIRST_NAME
Gail
ADDRESS
Penn State Hershey Heart and Vascular Institute Penn State College of Medicine 500 University Drive, MC H047 Hershey, PA 17033
Omega-6 and omega-3 oxylipins are implicated in soybean oil-induced obesity in mice (part II)
STUDY_SUMMARY
In this study we have compared the metabolic effects of conventional soybean oil to those of genetically modified Plenish soybean oil, that is low in linoleic acid and high in oleic acid. This work builds on our previous study showing that soybean oil, rich in polyunsaturated fats, is more obesogenic and diabetogenic than coconut oil, rich in saturated fats (PMID: 26200659). Here, in order to elucidate the mechanisms responsible for soybean oil induced obesity, we have performed the first ever metabolomics (in plasma and liver) and proteomics on the livers of mice fed the two soybean oil diets (plus those fed a high coconut oil and Viv chow diet). Our results show that the new high oleic soybean oil induces less obesity and adiposity than conventional soybean oil, but can cause hepatomegaly and liver dysfunction. Metabolomic analysis reveals that the hepatic and plasma metabolic profiles differ considerably between the two soybean oils. Hepatic C18 oxylipin metabolites of omega-6 (ω6) and omega-3 (ω3) fatty acids (linoleic and α-linolenic acid, respectively) in the cytochrome P450/soluble epoxide hydrolase pathway were found to correlate positively with obesity.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Omega-6 and omega-3 oxylipins are implicated in soybean oil-induced obesity in mice (part III)
STUDY_SUMMARY
In this study we have compared the metabolic effects of conventional soybean oil to those of genetically modified Plenish soybean oil, that is low in linoleic acid and high in oleic acid. This work builds on our previous study showing that soybean oil, rich in polyunsaturated fats, is more obesogenic and diabetogenic than coconut oil, rich in saturated fats (PMID: 26200659). Here, in order to elucidate the mechanisms responsible for soybean oil induced obesity, we have performed the first ever metabolomics (in plasma and liver) and proteomics on the livers of mice fed the two soybean oil diets (plus those fed a high coconut oil and Viv chow diet). Our results show that the new high oleic soybean oil induces less obesity and adiposity than conventional soybean oil, but can cause hepatomegaly and liver dysfunction. Metabolomic analysis reveals that the hepatic and plasma metabolic profiles differ considerably between the two soybean oils. Hepatic C18 oxylipin metabolites of omega-6 (ω6) and omega-3 (ω3) fatty acids (linoleic and α-linolenic acid, respectively) in the cytochrome P450/soluble epoxide hydrolase pathway were found to correlate positively with obesity.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
mTOR regulates metabolic adaptation of APCs in the lung microenvironment and controls the outcome of allergic inflammation
STUDY_SUMMARY
Antigen presenting cells (APCs) occupy diverse anatomical tissues, but their tissue-restricted homeostasis remains poorly understood. Here, working in mouse models of inflammation, we found that mTOR-dependent metabolic adaptation was required at discrete locations. mTOR was dispensable for DC homeostasis in secondary lymphoid tissues, but necessary to regulate cellular metabolism and accumulation of CD103+ DCs and alveolar macrophages in lung. Moreover, whilst numbers of mTOR-deficient lung CD11b+ DCs were not changed, they were metabolically reprogrammed to skew allergic inflammation from eosinophilic Th2 to neutrophilic Th17 polarity. The mechanism for this change was independent of translational control, but dependent on inflammatory DC which produced IL-23 and increased fatty acid oxidation. mTOR therefore mediates metabolic adaptation of APCs in distinct tissues, influencing the immunological character of allergic inflammation.
INSTITUTE
Emory University
LAST_NAME
Li; Gardinassi
FIRST_NAME
Shuzhao; Luiz
ADDRESS
Emory Woodruff Memorial Research Building, 1639 Pierce Dr NE, Atlanta, GA 30322
Omega-6 and omega-3 oxylipins are implicated in soybean oil-induced obesity in mice (part IV)
STUDY_SUMMARY
In this study we have compared the metabolic effects of conventional soybean oil to those of genetically modified Plenish soybean oil, that is low in linoleic acid and high in oleic acid. This work builds on our previous study showing that soybean oil, rich in polyunsaturated fats, is more obesogenic and diabetogenic than coconut oil, rich in saturated fats (PMID: 26200659). Here, in order to elucidate the mechanisms responsible for soybean oil induced obesity, we have performed the first ever metabolomics (in plasma and liver) and proteomics on the livers of mice fed the two soybean oil diets (plus those fed a high coconut oil and Viv chow diet). Our results show that the new high oleic soybean oil induces less obesity and adiposity than conventional soybean oil, but can cause hepatomegaly and liver dysfunction. Metabolomic analysis reveals that the hepatic and plasma metabolic profiles differ considerably between the two soybean oils. Hepatic C18 oxylipin metabolites of omega-6 (ω6) and omega-3 (ω3) fatty acids (linoleic and α-linolenic acid, respectively) in the cytochrome P450/soluble epoxide hydrolase pathway were found to correlate positively with obesity.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Omega-6 and omega-3 oxylipins are implicated in soybean oil-induced obesity in mice (part I)
STUDY_SUMMARY
In this study we have compared the metabolic effects of conventional soybean oil to those of genetically modified Plenish soybean oil, that is low in linoleic acid and high in oleic acid. This work builds on our previous study showing that soybean oil, rich in polyunsaturated fats, is more obesogenic and diabetogenic than coconut oil, rich in saturated fats (PMID: 26200659). Here, in order to elucidate the mechanisms responsible for soybean oil induced obesity, we have performed the first ever metabolomics (in plasma and liver) and proteomics on the livers of mice fed the two soybean oil diets (plus those fed a high coconut oil and Viv chow diet). Our results show that the new high oleic soybean oil induces less obesity and adiposity than conventional soybean oil, but can cause hepatomegaly and liver dysfunction. Metabolomic analysis reveals that the hepatic and plasma metabolic profiles differ considerably between the two soybean oils. Hepatic C18 oxylipin metabolites of omega-6 (ω6) and omega-3 (ω3) fatty acids (linoleic and α-linolenic acid, respectively) in the cytochrome P450/soluble epoxide hydrolase pathway were found to correlate positively with obesity.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
The samples are frozen biopsies of whilte subcutaneous adipose tissues (50 mg). Samples were collected from 4 hormone-sensitive lipase (HSL) WT patients (adipose insulin sensitive), 3 HSL heterozygote patients and 1 HSL KO patient.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Rats were subjected to bilateral rotator cuff tears of the right and left supraspinatus muscle. Muscles were harvested from each shoulder at 0, 10, 30, or 60 days post surgery.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Determining lipid composition of diabetic microvascular complication-prone tissues and comparing tissues levels to plasma levels. Samples are in addition to plasma and kidney tissue samples ran (shotgun lipidomics) in June-July 2014.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Characterization of Retinal Exudates in Coats Disease - lipid profile
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The aim of our study is to characterize the retinal lipid exudates through lipidomic assays. Lipidomic analysis will quantify and identify the retinal lipid exudates and provide a `lipid profile? of the exudates. The characterization of the retinal lipids will help in further understanding the pathogenesis of Coat?s disease. It may allow us to identify and therapeutically target a metabolic pathway to prevent retinal exudation abnormal in Coat?s disease.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Wild type (a/a) agouti mouse dams were randomized to one of three diets (control, mediterranean, western) two weeks prior to pairing with an agouti (Avy/a) sire. Diet exposure continued through pregnancy and lactation. All pups were weaned onto the control diet and then followed for metabolic phenotyping measures to 10 months of age. Comprehensive phenotyping (body composition, CLAMS, blood draw) was completed at 2, 4, and 8 months, with an OGTT at 8 months. Weekly weights were also recorded. The study examines whether prenatal dietary exposure to high fat diets (HFD) and bisphenol a (BPA, those groups will not be tested in this pilot) impacts metabolic programming in offspring as measured by hepatic steatosis, serum hormone levels, and epigenetic changes in hepatic lipid metabolism genes.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
8
TOTAL_SUBJECTS
6
STUDY_COMMENTS
Shotgun lipidomics will add insight into the potentially changing lipid composition of membranes in offspring following different prenatal diet exposures as a means of assessing risk of steatosis and metabolic changes.
LCR and HCR rats (from Nathan Qi's 2010 study) were dissected at rest or following 10 minutes of exercise. Mitochondria were isolated from frozen gastrocnemius skeletal muscle. Samples consist of these isolated mitochondria suspended in 50 uL of mitochondrial isolation buffer (IBM containing sucrose, salts, etc; see Katie Overmyer's notebook E, p~23).
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
4
TOTAL_SUBJECTS
12
STUDY_COMMENTS
Recommend extracting entire sample suspension, NOT pelleting and removing supernatant. Quantities are likely to be small (~1-3mg tissue each?) Protein assays were performed to estimate quantities; see Katie's notebook or contact Charles for these protein concentration estimates, but also RECOMMEND SAVING RESIDUAL PELLET to allow further normalization.
Plasma, kidney, sciatic nerve, and retina samples collected from control (db/m) and diabetic (db/db) mice. Samples snap frozen and stored at -80. Plasma volume measured and tissues weighed for lipid extraction.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
6
TOTAL_SUBJECTS
31
STUDY_COMMENTS
Plasma and kidney samples were originally prepped in June 2014 and analyzed on our first TripleTOF. George Michailidis has requested they be re-analyzed to compare results between platforms. N/R #91-111 are new samples that will be prepared for this experiment (n = 40). WHEN ANALYZING: need to separate by tissue (P, K, N, R) for imputation of missing values. Want raw data and normalized to IS.
The mice were injected via tail vein with either shBmal1 adenovirus or shLacz adenocirus as control (n=5 for each group), following 10 days of 5% ethanol diet feeding. Then the mice were dissected and liver tissues were flash freezed. 25mg liver tissues from each mouse of the same group were pooled.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Effects of rosiglitazone treatment on lipid composition
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Reprograming of 'white' to 'brite' adipocytes with higher oxidative capacity and improved endocrine function represents a potentially important approach to address the dysfunctional adipocyte phenotypes in obesity. We find that chronic treatment with the PPAR? agonist (rosiglitazone, 1 uM for 7days in vitro) in white human adipose tissue induced metabolic changes. Our trancriptome analysis showed that higher mitochondrial and peroxisomal fatty acid oxidation pathways and other genes involved in lipid metabolism including (re)esterification are induced by rosiglitazone treatment. To understand the biochemical basis of brite vs. white human adipocytes, we will perform comprehensive metabolomic profiling of control and rosiglitazone treated tissues using unbiased lipidomics approach.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Nonalcoholic steatohepatitis (NASH) changes with S.Q. Leptin administrations
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Samples are from individuals with documented fatty liver disease (NAFLD) from whom serum was drawn at baseline and after 1 and 12 months of S.Q. Leptin administrations. The effect of leptin on degree of steatosis and inflammation was assessed in liver biopsies at baseline and following 1 year of treatment.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Functional genomics study on Non Alcoholic fatty liver disease (NAFLD)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
In this experiment, vector , GCKR (WT), GCKR(P446L), PPP1R3B, TM6SF2 (WT and E167K) overexpression stable HuH-7_Lok cell lines as well as Non-target, GCKR shRNA (52621), PPP1R3B shRNA (2640), TM6SF2 shRNA (382426) knockdown HuH-7_Lok cell lines are used to do the lipidomics experiments 3 X 100 mm dishes of cells were seeded (1x106 cells/dish) for each cell line and incubated at 37? C for 24 hours, then replaced medium with delipidated serum DMEM medium. After 24 hours, treated with BSA-OA (200?M) for another 24 hours before the collection of cells Add 4mL/dish 50 mM ammonium acetate wash cells and then quench cells by adding liquid nitrogen covering all the surface of dish. Store the cell samples in -80?C freezer.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Functional genomics study on Non Alcoholic fatty liver disease (NAFLD) - part II
STUDY_TYPE
MS analysis
STUDY_SUMMARY
In this experiment, vector , GCKR (WT), GCKR(P446L), PPP1R3B, TM6SF2 (WT and E167K) overexpression stable HuH-7_Lok cell lines as well as Non-target, GCKR shRNA (52621), PPP1R3B shRNA (2640), TM6SF2 shRNA (382426) knockdown HuH-7_Lok cell lines are used to do the lipidomics experiments 3 X 100 mm dishes of cells were seeded (1x106 cells/dish) for each cell line and incubated at 37? C for 24 hours, then replaced medium with delipidated serum DMEM medium. After 24 hours, treated with BSA-OA (200?M) for another 24 hours before the collection of cells Add 4mL/dish 50 mM ammonium acetate wash cells and then quench cells by adding liquid nitrogen covering all the surface of dish. Store the cell samples in -80?C freezer.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Functional genomics study on Non Alcoholic fatty liver disease (NAFLD) - part III
STUDY_TYPE
MS analysis
STUDY_SUMMARY
In this experiment, vector , GCKR (WT), GCKR(P446L), PPP1R3B, TM6SF2 (WT and E167K) overexpression stable HuH-7_Lok cell lines as well as Non-target, GCKR shRNA (52621), PPP1R3B shRNA (2640), TM6SF2 shRNA (382426) knockdown HuH-7_Lok cell lines are used to do the lipidomics experiments 3 X 100 mm dishes of cells were seeded (1x106 cells/dish) for each cell line and incubated at 37? C for 24 hours, then replaced medium with delipidated serum DMEM medium. After 24 hours, treated with BSA-OA (200?M) for another 24 hours before the collection of cells Add 4mL/dish 50 mM ammonium acetate wash cells and then quench cells by adding liquid nitrogen covering all the surface of dish. Store the cell samples in -80?C freezer.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
ARetinal tissue knockout to study efflux of cholesterol (AGCA1/G1 double KO - TY and LysM cre)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
ABCA1 and AGCG1, which is important gene to efflux the cholesterol from the cell/tissue, are knocked out in specific retinal tissue. T:RPE specific, L:macrophage specific.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Retinal tissue knockout to study efflux of cholesterol (AGCA1/G1 double KO - TY and LysM cre) - part II
STUDY_TYPE
MS analysis
STUDY_SUMMARY
ABCA1 and AGCG1, which is important gene to efflux the cholesterol from the cell/tissue, are knocked out in specific retinal tissue. R:Rod specific, C:Cone specific.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Untargeted Lipidomics for hepatic lipid profile wild type versus knockout
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Use untargeted lipidomics to investigate differences in hepatic lipid profile between wild type and knockout mice. Mice were fed with high fat diet for 10 weeks and sacrificed under randomly fed condition. Liver were harvested freshly and frozen into liquid nitrogen immediately. Each sample was combined liver tissues from three individual mice in the same group.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Effect of fatty acids on macrophage (wild type versus knockout) lipid levels
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Macrophages from wild type or knockout mice with various treatments [none, BSA (control), palmitate + oleate, conditioned media from adipocytes treated with either BSA or palmitate + oleate). N=4/group.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
On day 1, seed 1 million cells/dish Huh7_Lok cells (vector, GCKR(WT), GCKR(P446L), Non-Target, GCKR KD and PPP1R3B/OE) in 100 mm dishes with DMEM complete medium and incubate at 37C for 24 h. On day 2, replace DMEM medium with delipidated serum medium for these cells and incubate for another 24 h. On day 3, add heated Oleic Acid-Albumin into each dish at final concentration of 200?M for 24h. On day 4, collect cells with Trypsin/EDTA lysis and count cells with automated cell counter and calculate total cell numbers in each sample, then centrifuge cells down and take out the supernatant and keep cells in -80 C freezer.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Lipodomics and Gestational bisphenol A (BPA) exposure
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Gestational BPA exposure in sheep induces metabolic phenotype in sheep characterized by peripheral insulin resistance and increased adipocyte size. Because insulin sensitivity can be regulated by various agents including free fatty acids (FFA), we hypothesize that gestational BPA exposure alters circulating FFA inducing dyslipidemia, a marker of metabolic disorder. Because saturated FFA is associated with insulin resistance, determination of the FFA profile in these species aid in understanding the underlying mechanism. Additionally, because of the non-monotonic nature of responses to BPA exposure dose response studies are also needed. This study will therefore assess plasma lipid profile in sheep exposed to three different doses of BPA prenatally and compared with untreated control animals
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
4
TOTAL_SUBJECTS
28
STUDY_COMMENTS
Metabolic disorders such as obesity and diabetes are currently widespread with epidemic proportions. Recent studies have implicated that these disorders have developmental basis due to maternal exposure to adverse insults including endocrine disruptors such as Bisphenol A (BPA). As BPA is present in maternal serum, amniotic fluid, cord blood taken at birth, placenta, colostrum and breast milk suggests that BPA has developmental impacts. In fact developmental BPA exposure have been linked to intrauterine growth restriction and low birth weight offspring, risk factors for adult cardiometabolic abnormalities. Animal models are helpful to study the effect of developmental BPA exposure and determine associated mechanisms.
Biomarkers for different types of Multiple Scelerosis (MS) (BMS vs SPMS lipidomics)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Metabolomic Analysis in Secondary Progressive and Benign MS. Preliminary data: We have conducted whole blood cell microarray comparing gene expression profile of 20 SPMS and 13 BMS patients. The data revealed significant increase in pathways involving iron ion binding, oxygen transporter activity and hemoglobin functions. Specifically, the identified down regulated genes are involved in interacting selectively and non-covalently with iron (Fe) ions. Heme has been described as a potent pro-inflammatory molecule that can induce multiple innate immune responses, and cause excessive iron and heme-induced oxidative stress and cell death. In the brain, it causes neurodegeneration. In addition, our microarray preliminary results also show a statistically significant increase in arachidonate 12-lipoxygenase activity in SPMS compared to benign MS. Specific aim. To validate metabolites and lipid biomarkers in serum samples from patients with benign and secondary progressive MS. Our central hypothesis is that the gene expression in various types of multiple sclerosis likely create a systematic metabolomic/lipidomic environment that leads to progression in MS. We plan to compare and contrast metabolomics in SP-MS to BMS patients using the innovative technology at the Metabolomics Research Core at the University of Michigan. By monitoring lipid and metabolite changes in SP and BMS patients, we aim to identify molecular processes and biomarkers of axonal damage for MS. Then, we plan to translate such metabolomic biomarkers to correlate with our rich clinical, immunological and imaging readouts. The goal of this project is to develop a blood-based test to differentiate SP-MS from BMS patients. To accomplish this, we will first identify the gene expression signature associated with of SP-MS. Then, we will correlate these gene expression changes with lipids and metabolite changes in the blood by metabolomic network analysis. Because metabolism is the final fingerprint of functionality and has been implicated in neurodegeneration, metabolomic network analysis can be used for refining the relationships between specific gene expression and metabolites and axonal damage in progressive MS. Ultimately, we hope to develop blood, CSF and stool-based assays, and use this comprehensive profile to predict susceptibility and progression of MS. This is a new and innovative idea, which will hope to lead to future diagnostic and therapeutic development in MS.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Human vitreous was collected in the OR at time of indicated surgery. No treatments were involved. Diagnoses are: epiretinal membranes (ERM); proliferative diabetic retinopathy (PDR); retinal detachment (RD)
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
The effect of acetate on intestinal microorganisms
STUDY_TYPE
MS analysis
STUDY_SUMMARY
8 week old B6 Male: HFD+ Glucose, 9 day feeding; Blood collection from tail every 3 days; mice were fed glycerol (control) or GTA with increasing concentrations; Day 1-3 0.1g/kg; Day 3-6 1g/kg; Day 6-9 6g/kg
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Hamsters were treated with Clindamycin, or a Saline, or nothing at all. After four days animals were sacrificed and their cecal contents were collected to record change in their Microbiome. Along with the Microbiome analysis we are also performing metabolomics analysis to understand the influence of change in the microbiome with the metabolic changes (if any). The cecal contents collected were frozen immediately (using liquid nitrogen) and was frozen in -80C until analysis.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Microbial ecology of nontuberculous mycobacteria (NTM) in cystic fibrosis (CF) sputum
STUDY_TYPE
MS analysis
STUDY_SUMMARY
These are sputum samples collected from 8 individuals with cystic fibrosis during the course of routine clinical care. They were initially stored at 4C for up to 24 hours then stored at -80C. No processing has been done to the sputum prior to freezing. For each individual there are sputum samples collected both before and after the individual had his or her first positive sputum culture for nontuberculous mycobacteria (NTM). The individuals experienced different clinical courses after their infection.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Diabetic heart adrenergic signaling and metabolism (STZ & Isoproterenol, High Fat)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
We are examing the effect of both diabetes and adrenergic activation on the metabolomic profile. STZ treatment was initiated 5 months before hearts were harvested. High fat/low fat diets were given for 13 weeks. All hearts were excised in the morning. For the STZ/isoproterenol experiment, mouse anesthesia was initiated with 4% isoflurane, and maintained with 2% and a homeothermic controller. After 5 min of equilibration, control and fasted mice were injected intraperitoneally with either saline (S) or 25ug/kg isoproterenol (I). After an additional 5 min, the whole heart was quickly excised, washed with ice-cold distilled water, dried off with a chem whipe, and flash frozen in liquid nitrogen. Hearts were stored at -80, and shipped using dry ice. The hearts from the high fat diet experiement were prepared in the same way, but no injection was given and total anesthesia time was 5min instead of 10min.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolic profiling of cyst fluid from patients with Intraductal Pancreatic Mucinous Neoplasm
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The pancreatic cyst fluids were collected using a syringe aspiration of the cyst fluid immediately after surgical resection of the lesion. The cyst fluid were then aliquoted and stored in -80C freezer until ready to use. We plan on performing untargeted metabolomics analysis on these pancreatic cyst fluid to find potential biomarkers that correlate with histopathological assessment and clinical behavior of these cystic lesions and thus to guide clinical management of patients.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Effect of genetic lesions on glioblastoma (NP, NPA, NPAI, NS)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The cells in this experiment are primary cells derived from tumors with various genetic lesions. The purpose of this experiment is to determine the effect of the genetic lesion IDH1m (mutant isocitrate dehydrogenase) on the metabolic state of the cell. Four replicates of NPA versus four replicates of NPAI suspension cell neurospheres will be compared in an untargeted manner to identify all possible metabolic differences between the two types of genetic lesions.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolomics of lean males given water, antibiotic cocktail (ANMV), or neomycin then exposed to ozone
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Mice were given either water, an antibiotic cocktail (ANMV), or Neomycin in their drinking water for two weeks to reduce bacterial load, and then exposed to air or to ozone (2ppm for 3hrs). 24 hours later, pulmonary mechanics and airway responsiveness was assessed, and blood was collected via cardiac puncture. Serum was isolated and immediately stored at -80 C for further analysis.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Analysis of SCFA in the fecal matter of wt and Orai1kO mice
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The gut microbiome participates in numerous physiological functions and is believed to be shaped by the host intestine. We report here an unsuspected prominent role of Orai1-mediated pancreatic acinar cell exocytosis in shaping the microbiome. Deletion of Orai1 in pancreatic acini of mature mice maintained on solid diet resulted in 60-70% mortality. The mice have severe bacterial burden with dysbiosis resulting in systemic inflammation and death. This occurs despite prominent Paneth cell hyperplasia and activation of the intestinal innate immune response. Secretion of and bacterial killing by pancreatic defensins are markedly reduced, resulting in microbiota with decreased diversity and increased pathogenic bacteria. Survival and weight gain are not rescued by digestive enzyme supplements, but are by broad-spectrum antibiotics and purified liquid diet. These findings reveal an unexpected profound role of pancreatic secretion in shaping the microbiome
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolomics has recently been used to document age-related changes in key metabolic pathways in laboratory animals and as a biomarker to predict age. We study the ecology, evolution, behavior, and physiology of wild North American red squirrels where we are able to follow individual squirrels across their lifetime from birth until death. We are beginning to document aging in this natural population and are interested in understanding whether there is a signature of aging using metabolomics. We collected plasma samples from the oldest female and male squirrels in our study population and also from an equivalent number of younger squirrels. We will use an untargeted approach to provide an assessment of what metabolites differ among very old and young squirrels. The aim of these analyses is to allow us to identify if the same metabolites that have been identified as biomarkers of advanced age from laboratory mice are also biomarkers of advanced age in red squirrels. After we complete these untargeted analyses, we aim to develop a metabolomics panel for this species so that we can use a more targeted approach to assess how the metabolic profiles of specific pathways (glucose/fatty acid metabolism, redox homeostasis) change with age in offspring exposed to increased perinatal stress in our study species.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
6
TOTAL_SUBJECTS
33
STUDY_COMMENTS
Metabolomics has recently been used to document age-related changes in key metabolic pathways in laboratory animals and as a biomarker to predict age. We study the ecology, evolution, behavior, and physiology of wild North American red squirrels where we are able to follow individual squirrels across their lifetime from birth until death. We are beginning to document aging in this natural population and are interested in understanding whether there is a signature of aging using metabolomics.
Metabolome, body composition, and muscle performance in children
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The purpose of this study is to determine potential relationships between plasma metabolome patterns and body composition in addition to muscle quality and muscular performance in children. Children ages 8 to 10 will complete body composition testing including BMI and skin fold measurements. An ultrasound machine will be used to determine cross-sectional area and echo intensity in the vastus lateralis and rectus femoris muscles as a measure of muscle quality. Isokinetic leg extension strength, power, and fatigability will be determined from a series of maximal knee extensions using an isokinetic dynamometer. An untargeted metabolomics test will be used on a single plasma sample from each subject in order to examine plasma metabolome
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
We intend to analyze 89 samples for Untargeted Metabolomics on patients with and without Polycystic Ovarian Syndrome(PCOS). Blood is drawn from patients at four different time points; 1st) 0 Timepoint at clamp 2nd) 270 Timepoint at clamp 3rd) 0 Timepoint at OGTT and 4th) 120 Timepoint at OGTT (a couple of samples were missing 120, but we included a 30 min sample and a 90 min sample and for some subjects OGTT samples are not included but not listed here). All samples are drawn in EDTA tubes at the Children's Hospital of Colorado. Collected blood is processed and frozen immediately at -80 degrees celcius.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
This is a double blind study, to measure short chain fatty acids in colons of mouse that have gone through bariatric surgery and the mouse that have gone through sham surgery (as control group). We would like to get a ratio of different types of fatty acids in the colons of these animals. This project looks at the effects of bariatric surgery on short chain fatty acids produced by microbiota ultimately the effects on the growth and suppression of breast cancer.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Effects of bariatric and antibiotic treatment surgery on mammary carcinogenesis
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The purpose of this study is to understand the effects of bariatric surgery on mammary carcinogenesis in C3 Tag (1) mouse model. My animals have gone through antibiotic treatments in drinking water vs. no abx in their water. Also animals have been though vertical sleeve gasteroctomy (VSG) vs sham surgery vs no surgery group. It is expected that these surgeries will affect the tumor proliferation and growth. One potential explanation can be the changes of SCFAs following the bariatric surgery.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolomics of rats after bariatric or sham surgery
STUDY_TYPE
MS analysis
STUDY_SUMMARY
We would like to examine the levels of amino acids in rats who have underwent bariatric (VSG, vertical sleeve gastrectomy) or sham (control) surgery. Plasma was collected after an overnight fast and once again after refeeding the rats for 2 hours.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
The aim of this study is to determine whether changes in CoA degradation affect the composition of the acylcarntine pool in the liver. 7 wild-type and 7 Nudt7 knockout male mice (10-16 weeks of age) on a mixed background were fasted for 24h and allowed to refeed for 12-14hours before removing the liver. The liver samples were flash-frozen and stored at -80C until used.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Microbial changes following fecal microbiota transplantation in patients with recurrent C. difficile infection
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Fecal samples were collected from patients with recurrent Clostridium difficile infection before and after treatment with fecal microbiota transplantation. Fecal samples were frozen immediately after collections, and later put into ~50mg aliquots for later analysis (at -80 C).
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Measuring SCFA in mice gut following colonization by C. difficile
STUDY_TYPE
MS analysis
STUDY_SUMMARY
3 cages of 5-8 week old C57B/6 mice were placed on the antibiotic cefoperazone for 10 days followed by 2 days of reovery on plain water. One cage remained on plain water the entire time. Of the three antibiotic treated cages. One was mock infected (uninfected control), one was infected with C. difficile strain VPI 10463, while the other was infected with C. difficile strain 630. Twenty-four hours after the infection the mice were eutanized and the ceal content was collected and snap frozen in liquid nitrogen. Samples were stored in the -80 until analysis.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Murine bile acid profiles during CDI R20291 infection
STUDY_TYPE
MS analysis
STUDY_SUMMARY
We are interested in understanding the bile acid profiles in cecal content from mice challeneged with R20291 C. difficle spores. We are also interested in the bile acid profiles of mice that are administered Ursodiol (UDCA) or vehcile (corn oil) during C. difficile infection. In vitro Ursodiol (UDCA) has significant impacts on germination and growth of C. difficile R20291.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolic change in macrophages after efferocytosis
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Study metabolic pathway alteration in macrophages after efferocytosis (when macrophages eating apoptotic cells). Peritoneal macrophages were purified and plated in the cell-culture dishes. After culturing overnight. Apoptotic cells were overlayed to macrophages for 2 hours, then un-engulfed cells were removed through washing. Macrophages were left in the plate for another 4 hours before being lifted from the plate.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolic change in macrophages after efferocytosis (part II)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The goal of the experiment is to study metabolic pathway alteration in macrophages after efferocytosis (when macrophages eating apoptotic cells). Peritoneal macrophages were purified and plated in the cell-culture dishes. After culturing overnight. Apoptotic cells were overlayed to macrophages for 2 hours, then un-engulfed cells were removed through washing. Macrophages were left in the plate for another 4 hours before being lifted from the plate.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Human patients were enrolled in a bariatric weight loss clinic and followed. Patients were male and female, normoglycemic,pre-diabetic and diabetic and with and without neuropathy. One 500 ul aliquot will be submitted for both untargeted metabolomics and shotgun lipidomics.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolomics of intensive weight management clinic (IWMC) weight loss
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Human patients were enrolled in a weight loss clinic and followed. Patients were male and female, normoglycemic,pre-diabetic and diabetic and with and without neuropathy.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
BeWo cells were plated in 100mm x 20mm cell culture plates and allowed to attach and acclimate for 24 hours. Cell culture media was then replaced with media containing mono(2-ethylhexyl)phthalate (MEHP) at either 90 or 180 micromolar concentrations or vehicle control (DMSO, 0.05% by volume). Cells were exposed for 24 hours followed by collection of cell media which was flash frozen in liquid nitrogen and then placed on dry ice. Cells were washed with sodium acetate and then immediately flash frozen by addition of ~8mL of liquid nitrogen to tissue culture plate. All samples were stored at -80 degrees C.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Pregnant rats were treated for 5 days with 100mg/kg/day DEHP or vehicle control (corn oil) via a wafer which the rats consumed orally. After the fifth treatment, rats were euthanized and uterine horns were dissected. Amniotic fluid was collected from the gestational sac via syringe and collected into 1.5mL tubes. Tubes were then stored at -80 celsius
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Pregnant rats were treated for 5 days with 100mg/kg/day DEHP or vehicle control (corn oil) via a wafer which the rats consumed orally. After the fifth treatment, rats were euthanized and uterine horns were dissected. Amniotic fluid was collected from the gestational sac via syringe and collected into 1.5mL tubes. Tubes were then stored at -80 celsius.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Pregnant mice were treated for 14 days (from GD 0.5-13.5) with 125mg/kg/day DEHP or vehicle control (corn oil) via oral gavage. After the last treatment, mice were euthanized and placenta were removed and flash frozen in liquid nitrogen. Placentas were then stored at -80 celsius.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Thermal modalities are commonly used in sports medicine to affect tissue healing. Cold therapy is commonly used modalities, but the metabolic changes to muscle after cooling are not known. The objective of this study is to look at the effect of cooling on muscle metabolites and gene expression. There are a total of 8 subjects in the study. Each subject had an ice cup cryotherapy treatment ("cool" samples) to one leg for 15 minutes, and the other leg served as the control ("cntrl" samples). Two hours after the application of cryotherapy, a biopsy was taken from each thigh muscle. Muscle was minced with scissors and quickly snap frozen in liquid nitrogen.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
10
TOTAL_SUBJECTS
8
STUDY_COMMENTS
We would like to run the TCA Plus Analysis on each of the samples. For the statistical analysis, we would normalize the cool side to the ctrl side, and look at the relative change in metabolite abundance as a result of the cooling procedure. only used in sports medicine to affect tissue healing.
Comparison of the metabolome and lipidome of wild type and mdx/mTR mice
STUDY_TYPE
MS analysis
STUDY_SUMMARY
There are two groups of mice in the study, wild type mice (WT) and mdx/mTR mice (mdx or mdx/mTR) that are a model of musclar dystrophy. We collected the tibialis anterior muscles from these mice (N=6 in each group), and would like to perform TCA-plus analysis and shotgun lipidomics analysis on the mice, and compare across the two groups.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Rat Retinal Detachment Metabolomics Timecourse (part II)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Detachments were created in adult male Brown-Norway rats (300?400 g; Charles River Laboratories, Wilmington, MA). Briefly, rodents were anesthetized with a 50:50 mix of ketamine/xylazine, and pupils were dilated with topical phenylephrine (2.5%) and tropicamide (1%). A 20-gauge microvitreoretinal blade was used to create a sclerotomy 2 mm posterior to the limbus, carefully avoiding lens damage. A subretinal injector (Glaser, 32-gauge tip; BD Ophthalmic Systems, Franklin Lakes, NJ) was introduced through the sclerotomy into the vitreous cavity and then through a peripheral retinotomy into the subretinal space. Sodium hyaluronate (10 mg/mL, Healon OVD; Abbott Medical Optics, Uppsala, Sweden) was slowly injected to detach the neurosensory retina from the underlying RPE. In all experiments, approximately one third to one half of the neurosensory retina was detached. Detachments were created in the left eye. The right eye served as the control, with all the steps of the procedure performed except for introduction of the subretinal injector and injection of the sodium hyaluronate. At varying intervals after creation of the detachment, the animals were euthanatized, and the eyes were enucleated.The retina was then dissected away from the retinal pigment epithelium taking just the detached portion in those eyes experimentally detached. All experiments were performed in accordance with the ARVO Statement for the Use of Animals in Ophthalmic and Vision Research and the guidelines established by the University Committee on Use and Care of Animals of the University of Michigan. Detachments were created in adult male Brown-Norway rats (300?400 g; Charles River Laboratories, Wilmington, MA).
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
10
TOTAL_SUBJECTS
27
STUDY_COMMENTS
All experiments were performed in accordance with the ARVO Statement for the Use of Animals in Ophthalmic and Vision Research and the guidelines established by the University Committee on Use and Care of Animals of the University of Michigan. Detachments were created in adult male Brown-Norway rats (300?400 g; Charles River Laboratories, Wilmington, MA).
N/NIH rats were selected for either low (LRT) or high (HRT) response to training. Rats at 2 year of age were trained for 8 weeks with an improvement in oxidative capacity. Selection was also performed for high (HCR) or low (LCR) intrinsic running capacity. Young and old animals are compared to 12 week old animals.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Plasma Nucleotide/adenosine concentrations in patiens with scleroderma depending on exercise
STUDY_TYPE
MS analysis
STUDY_SUMMARY
This experiment was performed using the following cohorts: 1) healthy controls, 2) patients with scleroderma at low risk for pulmonary hypertension, 3) pateints with scleroderma at high risk for pulmonary hypertension ("SSc Cath"). Whole blood was drawn directly into stop soilution (1:1 ratio) at rest and again at peak exercise for each human subject. The samples were processed to plasma by MCRU and stored at -80 in the Biorepository.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Untargeted metabolomics and lipidomics of scleroderma PAH discovery cohort
STUDY_TYPE
MS analysis
STUDY_SUMMARY
This experiment was performed using the following cohorts: 1) healthy controls, 2) patients with scleroderma at low risk for pulmonary hypertension, 3) pateints with scleroderma at high risk for pulmonary hypertension who underwent a catheterization and were found to have normal pressures, borderline elevated pressures or pulmonary arterial hypertensino (PAH). Whole blood was drawn directly into EDTA tubes at rest and again at peak exercise for each human subject. The samples were processed to plasma by MCRU and stored at -80 in the Biorepository.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Differences in metabolite profiles and antioxidant activities between wild and cultivated black soybeans evaluated by a correlation analysis
STUDY_SUMMARY
Non-targeted metabolic profiling of 26 soybean varieties using liquid chromatography-mass spectrometry (LC-MS) including 15 wild black soybeans (WBS) and 11 cultivated black soybeans (CBS), combined with multivariate analysis, revealed significant differences in 25 differential metabolites
INSTITUTE
KIST
LAST_NAME
Xu
FIRST_NAME
Jiuliang
ADDRESS
saimdang-ro 679, Gangneung, Gangwon, 213510, Korea, South
Metabolite analysis of regional neural stem/progenitor cells
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The developing mammalian brain generates a variety of Neural Progenitor Cells (NPCs). Primary NPCs throughout the neuraxis are derived from the ventricular zone. Intermediate progenitor cells (IPCs) are produced uniquely in the telencephalon and contribute extensively to the neurons that comprise the cerebral cortex and basal ganglia. It is known that the fate of the diverse NPC populations is determined by the interplay of transcription factors and regulation by regional humoral cues. However, despite our recent appreciation that nutrient-regulated intracellular metabolic milieu (pO2, energy, and redox state) significantly influence cell fate, an unexplored area is whether NPCs have intrinsic metabolic identity, and if so, the mechanism by which molecular metabolism contributes to brain development.Little is known however, if intrinsic differences in cellular metabolism of regional NPCs make certain NPCs susceptible while others resistant to genetic and environmental insults. We conjectured that regional (fore-and hindbrain) NPCs are metabolically distinct.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolites of human neurons and stem cells (siNeuron metabolomics)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
There are a total of four samples each for this analysis. Each sample consists of the cells grown on three 10 cm culture plates. Each plate should have 2x106 cells for a total of 6x106 cells per sample when all three plates are combined. The first sample is undifferentiated human embryonic stem cells, the second sample is human glutamatergic neurons derived from those human embryonic stem cells, the third sample is undifferentiated human induced pluripotent stem cells and the fourth sample is human glutamatergic neurons derived from those human induced pluripotent stem cells.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
From Lawson et al., Obesity 2015 (PMID: 25865294). Methods: A randomized, placebo-controlled crossover study of single-dose intranasal oxytocin (24 IU) in 25 fasting healthy men was performed. After oxytocin/placebo, subjects selected breakfast from a menu and were given double portions. Caloric content of food consumed was measured. Visual analog scales were used to assess appetite, and blood was drawn for appetite-regulating hormones, insulin, and glucose before and after oxytocin/placebo. Indirect calorimetry assessed resting energy expenditure (REE) and substrate utilization. Here, T0 refers to immediately before OXT or Placebo was administered (fasting), and T55 refers to 55 minutes post-administration (fasting, immediately pre-meal).
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Looking for changes in lipid levels with knock out of ACADM (shACADM)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
GSC 8-11 cells (20 million) were transduced with lentivirus coding for shACADM 4, 6, or scr (control). ACADM is an enzyme responsible for the metabolism of medium chain fatty acids (C4-C12). A round of selection was performed using puromycin to ensure only cells that had been transduced survived. Knockdown of ACADM was confirmed via western blot. Pellets were collected by centrifuging cells for 10 min at max speed. The pellets were washed and each sample was split into quadruplicate.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolic Adaptations to Chronic and Acute Exercise in Overweight Adults (ATX-Study) preliminary data
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The primary purpose of this study is to examine the effects of chronic exercise training and an acute session of exercise on key risk factors associated with Metabolic Syndrome (e.g., glucose tolerance, blood lipid profile, and blood pressure) and alterations in subcutaneous adipose tissue structure and metabolic function in overweight adults. Human adipose tissue samples collected before, and one hour after a 1h exercise session at ~65% VO2max (maximal oxygen uptake)
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Lipidomics pilot project for mice exposure to bisphenol A and high fat diets
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Wild type (a/a) agouti mouse dams were randomized to one of three diets (control, Mediterranean, western) two weeks prior to pairing with an agouti (Avy/a) sire. Diet exposure continued through pregnancy and lactation. All pups were weaned onto the control diet and then followed for metabolic phenotyping measures to 10 months of age. Comprehensive phenotyping (body composition, CLAMS, blood draw) was completed at 2, 4, and 8 months, with an OGTT at 8 months. Weekly weights were also recorded. The study examines whether prenatal dietary exposure to high fat diets (HFD) and bisphenol a (BPA, those groups will not be tested in this pilot) impacts metabolic programming in offspring as measured by hepatic steatosis, serum hormone levels, and epigenetic changes in hepatic lipid metabolism genes. Shotgun lipidomics will add insight into the potentially changing lipid composition of membranes in offspring following different prenatal diet exposures as a means of assessing risk of steatosis and metabolic changes.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Six strain/genotype combinations (BKS wt, BKS db/+, ?) were fed control (5LOD) or high fat (54 % lard) chow from 5 to 36 weeks of age. Longitudinal changes in small and large nerve fiber function, glucose tolerance, fasting blood glucose, body weight etc. were assessed in all groups
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Absolute Quantification of 180 metabolites in serum from african american and european american in prostate cancer and case control samples
STUDY_SUMMARY
Metabolite concentrations were obtained in prostate cancer and case control plasma samples from AA and EA individuals using the AbsoluteIDQ kit p180 (Biocrates Life Science AG, Austria) according to the manufacturer’s instructions. The analysis was performed using a QTRAP 6500 LC/MS/MS System (AB SCIEX, USA) equipped with an electrospray ionization source, Agilent G1367B autosampler and the Analyst 1.51 software (AB SCIEX, USA).
metabolome in a group of AA and EA matched pairs of prostate cancer (PCa) and benign adjacent tissues
STUDY_SUMMARY
10 µL of suspended samples was injected and analyzed using a 6495 triple quadrupole mass spectrometer (Agilent Technologies, Santa Clara, CA) coupled to a HPLC system (Agilent Technologies, Santa Clara, CA) via Multiple reaction monitoring (MRM) of a total of 240 endogenous water soluble metabolites for steady-state analyses of samples. Those 240 compounds monitored were chosen due to their involvement in central pathways important in a number of malignancies. Source parameters were as follows: Gas temperature was 250 °C; Gas flow was 14 l/min; Nebulizer was 20psi; Sheath gas temperature was 350 °C; Sheath gas flow was 12 l/min; Capillary was 3000 V positive and 3000 V negative; Nozzle voltage was 1500 V positive and 1500 V negative. Approximately 8–11 data points were acquired per detected metabolite. Samples were delivered to the MS via normal phase chromatography using either a 4.6 mm i.d ×10 cm Amide XBridge HILIC column (Waters) or a Luna 3µ NH2 100A (Phenomenex) at 300 µL/min
An untargeted metabolomics approach was utilized to determine urinary metabolites that could serve as small molecule biomarkers for treatment response to standard tuberculosis treatment. However, the majority of metabolites that most accurately distinguished patient samples at time of diagnosis from those at one month after the start of therapy lacked structural identification. The detection of unknown metabolite structures is a well-known limitation of untargeted metabolomics, and underscores a need for continued elucidation of novel metabolite structures. In this study, we sought to define the structure of a urine metabolite with an experimentally determined mass of 202.1326 Da, classified as molecular feature (MF) 202.1326. A hypothesized structure of N1-acetylisoputreanine was developed for MF 202.1326 using in silico tools and liquid chromatography-tandem mass spectrometry (LC-MS/MS). In the absence of a commercial standard, synthetic N1-acetylisoputreanine was generated using enzymatic and chemical synthesis and LC-MS/MS was used to confirm the structure of MF 202.1326 as N1-acetylisoputreanine, a proposed terminal polyamine catabolite that had not been previously detected in biological samples. Further analysis demonstrated that N1-acetylisoputreanine and an alternative form of this metabolite, N1-acetylisoputreanine-γ-lactam, are both present in human urine and are likely end-products of polyamine metabolism.
Identifying metabolic adaptations characteristic of multiple myeloma cells via mass spectrometry-based metabolite profiling from Peripheral Plasma
STUDY_SUMMARY
Will be assessing the untargeted metabolomic profiles of high risk versus low risk smoldering myeloma patients based on peripheral blood plasma, bone marrow plasma and Cd138+ plasma cells. Peripheral Plasma ms5972
INSTITUTE
Mayo Clinic
LAST_NAME
Gonsalves
FIRST_NAME
Wilson
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Identifying metabolic adaptations characteristic of multiple myeloma cells via mass spectrometry-based metabolite profiling from Bone Marrow Plasma
STUDY_SUMMARY
Will be assessing the untargeted metabolomic profiles of high risk versus low risk smoldering myeloma patients based on peripheral blood plasma, bone marrow plasma and Cd138+ plasma cells. Bone Marrow Plasma ms5973
INSTITUTE
Mayo Clinic
LAST_NAME
Gonsalves
FIRST_NAME
Wilson
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Identifying metabolic adaptations characteristic of multiple myeloma cells via mass spectrometry-based metabolite profiling from (CD138+ Plasma Cells)
STUDY_SUMMARY
Will be assessing the untargeted metabolomic profiles of high risk versus low risk smoldering myeloma patients based on peripheral blood plasma, bone marrow plasma and Cd138+ plasma cells. Cd138+ plasma cells ms5974
INSTITUTE
Mayo Clinic
LAST_NAME
Gonsalves
FIRST_NAME
Wilson
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Insights into myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) phenotypes through comprehensive metabolomics
STUDY_TYPE
Observational
STUDY_SUMMARY
The pathogenesis of ME/CFS, a disease characterized by unexplained debilitating fatigue, cognitive dysfunction, sleep disturbances, orthostatic intolerance, fever, lymphadenopathy and irritable bowel syndrome (IBS), is poorly understood. There are no validated diagnostic tests or interventions to mitigate disease. Here we report association modeling, biomarker discovery, biochemical enrichment analysis and topological network visualization of plasma metabolomic, fecal bacterial metagenomic and clinical data from 50 ME/CFS patients and 50 healthy controls. Through targeted and untargeted metabolomics analyses we confirm earlier reports of specific alterations in plasma levels of choline, carnitine and complex lipid metabolism in ME/CFS. We also demonstrate that patients with ME/CFS and IBS have a unique metabolomic profile that includes increased plasma levels of ceramide, a waxy lipid implicated in suppression of electron transport, insulin and leptin resistance and apoptosis. Integration of fecal metagenomic and plasma metabolomic data resulted in a stronger predictive model of ME/CFS (cross-validated AUC=0.836) than either metagenomic (cross-validated AUC=0.745) or metabolomic (cross-validated AUC=0.820) analysis alone. Our findings may provide insights into the pathogenesis of ME/CFS and ME/CFS subtypes, and suggest pathways for the development of diagnostic and therapeutic strategies.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
Key: mecfs : 1 in this column indicates case, while 0 indicates control Ibs: 1 in this column indicates the patient does have disease, 0 indicates free of ibs
Insights into myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) phenotypes through comprehensive metabolomics
STUDY_TYPE
Observational
STUDY_SUMMARY
The pathogenesis of ME/CFS, a disease characterized by unexplained debilitating fatigue, cognitive dysfunction, sleep disturbances, orthostatic intolerance, fever, lymphadenopathy and irritable bowel syndrome (IBS), is poorly understood. There are no validated diagnostic tests or interventions to mitigate disease. Here we report association modeling, biomarker discovery, biochemical enrichment analysis and topological network visualization of plasma metabolomic, fecal bacterial metagenomic and clinical data from 50 ME/CFS patients and 50 healthy controls.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
Key: mecfs : 1 in this column indicates case, while 0 indicates control Ibs: 1 in this column indicates the patient does have disease, 0 indicates free of ibs
Insights into myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) phenotypes through comprehensive metabolomics (part III))
STUDY_TYPE
Observational
STUDY_SUMMARY
The pathogenesis of ME/CFS, a disease characterized by unexplained debilitating fatigue, cognitive dysfunction, sleep disturbances, orthostatic intolerance, fever, lymphadenopathy and irritable bowel syndrome (IBS), is poorly understood. There are no validated diagnostic tests or interventions to mitigate disease. Here we report association modeling, biomarker discovery, biochemical enrichment analysis and topological network visualization of plasma metabolomic, fecal bacterial metagenomic and clinical data from 50 ME/CFS patients and 50 healthy controls. Through targeted and untargeted metabolomics analyses we confirm earlier reports of specific alterations in plasma levels of choline, carnitine and complex lipid metabolism in ME/CFS. We also demonstrate that patients with ME/CFS and IBS have a unique metabolomic profile that includes increased plasma levels of ceramide, a waxy lipid implicated in suppression of electron transport, insulin and leptin resistance and apoptosis. Integration of fecal metagenomic and plasma metabolomic data resulted in a stronger predictive model of ME/CFS (cross-validated AUC=0.836) than either metagenomic (cross-validated AUC=0.745) or metabolomic (cross-validated AUC=0.820) analysis alone. Our findings may provide insights into the pathogenesis of ME/CFS and ME/CFS subtypes, and suggest pathways for the development of diagnostic and therapeutic strategies.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
Key: MECFS: 1 in this column indicates case, while 0 indicates control IBS: 1 in this column indicates the patient does have disease, 0 indicates free of IBS
Insights into myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) phenotypes through comprehensive metabolomics (part IV)
STUDY_TYPE
Observational
STUDY_SUMMARY
The pathogenesis of ME/CFS, a disease characterized by unexplained debilitating fatigue, cognitive dysfunction, sleep disturbances, orthostatic intolerance, fever, lymphadenopathy and irritable bowel syndrome (IBS), is poorly understood. There are no validated diagnostic tests or interventions to mitigate disease. Here we report association modeling, biomarker discovery, biochemical enrichment analysis and topological network visualization of plasma metabolomic, fecal bacterial metagenomic and clinical data from 50 ME/CFS patients and 50 healthy controls. Through targeted and untargeted metabolomics analyses we confirm earlier reports of specific alterations in plasma levels of choline, carnitine and complex lipid metabolism in ME/CFS. We also demonstrate that patients with ME/CFS and IBS have a unique metabolomic profile that includes increased plasma levels of ceramide, a waxy lipid implicated in suppression of electron transport, insulin and leptin resistance and apoptosis. Integration of fecal metagenomic and plasma metabolomic data resulted in a stronger predictive model of ME/CFS (cross-validated AUC=0.836) than either metagenomic (cross-validated AUC=0.745) or metabolomic (cross-validated AUC=0.820) analysis alone. Our findings may provide insights into the pathogenesis of ME/CFS and ME/CFS subtypes, and suggest pathways for the development of diagnostic and therapeutic strategies.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
Key: MECFS: 1 in this column indicates case, while 0 indicates control IBS: 1 in this column indicates the patient does have disease, 0 indicates free of IBS
The goal of this study was to characterize the metabolic impact manifested in mouse lung following acute ozone exposure, comparing differential effects experienced by lean and obese model mice.
Analysis of blood plasma lipid composition in patients with diabetic kidney disease In this untargeted lipidomics study we are comparing the lipidomics profile of progressors versus nonprogressors. A subgroup of patients have a follow up samples and therefore their baseline data are comared to the follow up visit data.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Dynamics of metabolism, proliferation and differentiation in Toxoplasma gondii mutants deficient in glycolysis and gluconeogenesis
STUDY_TYPE
Time course 13C labeling of Toxoplasma gondii using glucose and glutamine
STUDY_SUMMARY
The focus of this study was to profile the metabolic fates of glucose and glutamine in wild type, glycolytic mutant (hexokinase KO) and gluconeogenesis mutant (PEPCK1 KO) tachyzoite stage T. gondii parasites. 13C6-glucose and 13C5-15N1-glutamine were used as metabolic tracers. Metabolites from glycolysis, pentosephosphate pathway and Kerbs cycle were identified and their isotopomer abundance was quantified in order to visualize metabolic flux across the indicated pathways. A time course (from 0 minutes to 120 minutes) analysis was carried out in the labeling experiments. Here, host cell free extracellular tachyzoite stage T. gondii parasites were used.
INSTITUTE
CSIR-National Chemical Laboratory
DEPARTMENT
Biochemical Sciences Division
LABORATORY
Molecular Parasitology Laboratory
LAST_NAME
Shanmugam
FIRST_NAME
Dhanasekaran
ADDRESS
Dr. Homi Bhabha Road, Pune, 411008, Maharashtra, India
Looking for changes in lipid levels with knock out of ACADM (shACADM)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
GSC 8-11 cells (20 million) were transduced with lentivirus coding for shACADM 4, 6, or scr (control). ACADM is an enzyme responsible for the metabolism of medium chain fatty acids (C4-C12). A round of selection was performed using puromycin to ensure only cells that had been transduced survived. Knockdown of ACADM was confirmed via western blot. Pellets were collected by centrifuging cells for 10 min at max speed. The pellets were washed and each sample was split into quadruplicate.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
2 hydroxyglutarate prodution in neurospheres from IDH1 mouse glioma model #2
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Evaluation of 2HG and a-ketoglutarate in tumor neurospheres (NS) genertated from the mice brain tumors haboring specific genetic lesions: NRAS overexpression, p53 knockdown plus or minus IDH1 mutated and ATRX knockdown.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
We are interested in using both spontaneous and stimulated Raman microscopy to visualize these metabolomic changes as spectral alterations. We have two isogneic cell lines of normal human astrocytes differing only by a point mutation in the IDH-1 gene. We will work with the metabolomics core to elucidate the changes in central metabolism and lipid synthesys in an effort to determine the precise biochemical alterations underlying observed spectral differences. We wil then use a selective inhibitor of the IDH1 R132H to demonstrate to attempt to return TCA metabolome and lipidome to WT phenotype. Lastly, we will use a cell-permeablized variant of 2HG (2R-octyl-alpha-hydroxyglutarate) to recaptitulate the R132H mutant phenotype in wild-type cells, providing strong evidence that 2HG accumulation uderlies the metabolomic (and thus, spectral) changes observed.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
2
TOTAL_SUBJECTS
3
STUDY_COMMENTS
The IDH-1 R132H mutation in low grade gliomas preceptitates oncogenesis through a neomorphic enzyme function: the reduction of alpha-ketoglutarate (aKG) to 2-hydroxygutarate (2HG). 2HG accumukates to extremely high (~100mM) concentrations in IDH1 mutant cells and has substantial, predictable metabolic effects, including inhibition of a-KG dependent dioxygenases and hypermethylation of histones and chromatin.
We are interested in using both spontaneous and stimulated Raman microscopy to visualize these metabolomic changes as spectral alterations. We have two isogneic cell lines of normal human astrocytes differing only by a point mutation in the IDH-1 gene. We will work with the metabolomics core to elucidate the changes in central metabolism and lipid synthesys in an effort to determine the precise biochemical alterations underlying observed spectral differences. We wil then use a selective inhibitor of the IDH1 R132H to demonstrate to attempt to return TCA metabolome and lipidome to WT phenotype. Lastly, we will use a cell-permeablized variant of 2HG (2R-octyl-alpha-hydroxyglutarate) to recaptitulate the R132H mutant phenotype in wild-type cells, providing strong evidence that 2HG accumulation uderlies the metabolomic (and thus, spectral) changes observed.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolic profiling of cyst fluid from patients with Intraductal Pancreatic Mucinous Neoplasm
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The pancreatic cyst fluids were collected using a syringe aspiration of the cyst fluid immediately after surgical resection of the lesion. The cyst fluid were then aliquoted and stored in -80C freezer until ready to use. We plan on performing untargeted metabolomics analysis and unknown lipid analysis and identification on these pancreatic cyst fluid to find potential biomarkers that correlate with histopathological assessment and clinical behavior of these cystic lesions and thus to guide clinical management of patients. Abbreviations: IPMN - Intraductal Pancreatic Mucinous Neoplasm; MCN - mucinous cystic neoplasm; SCA - serous cystadenoma.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolic analysis of Normal Mouse Lung Fiboblasts with/without TGFbeta treatment
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Glycolysis/TCA/Nucleotide analysis (especially interested in alpha-ketoglutarate) and NAD+ and related metabolite analysis for parp1 ko and parp1 wild type lung tissue after saline or bleomycin treatment
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
We are interested in understanding the bile acid profiles from the feces of fecal microbiota transplant FMT patients that successfully recover from recurrent C. difficile infection. We have are submitting fecal samples from patients prior to their FMT and post FMT. We are also interested in the bile acid profiles of the donor stool that is used in successful transplants. Bile acids are important for C. difficile spore germination and outgrowth.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Detachments were created in adult male Brown-Norway rats (300?400 g; Charles River Laboratories, Wilmington, MA). Briefly, rodents were anesthetized with a 50:50 mix of ketamine/xylazine, and pupils were dilated with topical phenylephrine (2.5%) and tropicamide (1%). A 20-gauge microvitreoretinal blade was used to create a sclerotomy 2 mm posterior to the limbus, carefully avoiding lens damage. A subretinal injector (Glaser, 32-gauge tip; BD Ophthalmic Systems, Franklin Lakes, NJ) was introduced through the sclerotomy into the vitreous cavity and then through a peripheral retinotomy into the subretinal space. Sodium hyaluronate (10 mg/mL, Healon OVD; Abbott Medical Optics, Uppsala, Sweden) was slowly injected to detach the neurosensory retina from the underlying RPE. In all experiments, approximately one third to one half of the neurosensory retina was detached. Detachments were created in the left eye. The right eye served as the control, with all the steps of the procedure performed except for introduction of the subretinal injector and injection of the sodium hyaluronate. At varying intervals after creation of the detachment, the animals were euthanatized, and the eyes were enucleated.The retina was then dissected away from the retinal pigment epithelium taking just the detached portion in those eyes experimentally detached. All experiments were performed in accordance with the ARVO Statement for the Use of Animals in Ophthalmic and Vision Research and the guidelines established by the University Committee on Use and Care of Animals of the University of Michigan.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
6.5 X 10^6 cells were plated in 10 cm Tissue Culture dishes and allowed to recover overnight at 37 degrees and 5% CO2. In the am, supernatant was removed, and 12 mL of medium containing either Murine Norovirus-1 (MNV) at an MOI=5 or medium containing a v/v match of mock lysate was added to the cells. Plates were rocked on ice for 1 hour, then cells were washed 3X with cold DPBS++, and plain medium as added to cells. Plates were then incubated for 7.5 hours at 37 degrees and 5% CO2. Cells were washed with 12 mL of 150 mM Ammonium Acetate, swirled 8 times, and immediately quenched with liquid nitrogen. Cells were then frozen at -80 degrees.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
2
TOTAL_SUBJECTS
1
STUDY_COMMENTS
BIOHAZARD - MURINE NOROVIRUS - SHOULD BE ENTIRELY NON-INFECTIOUS DUE TO THE LIQUID NITROGEN, BUT PLEASE HANDLE AND DISPOSE OF IN BIOHAZARD WASTE. IMPORTANT NOTE: I request that the metabolites of the TCA+ assay that are to be assessed quantitatively please be sure to include ATP, ADP, AMP, NAD, NADH, NADP, NADPH, E4P, S7P, 6PG, G3P H6P and Lactate. Also, I would request that both reduced and oxidized Glutathione as well as Fructose 1,6-bisphosphate be included in the non-quantitative data.
Purine and TCA measurements in salt sensitive (SS) hypertension
STUDY_TYPE
MS analysis
STUDY_SUMMARY
SS rats were surgically implanted with a chronic servo-control cuff, the purpose of which is to maintain normal pressure to the left kidney while the right kidney is exposed to high blood pressure. After 7 days of high salt treatment, which induces high blood pressure in the SS rat, rats were anesthetized with pentobarbital, kidneys were flushed and removed. The renal medulla was separated from the cortex using scissors, and the renal medullas were frozen in liquid nitrogen and stored at -80 C.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Deubiquitinase inhibitor compound C6 effect on cellular metabolism
STUDY_TYPE
MS analysis
STUDY_SUMMARY
6.0 X 10^6 cells were plated in 10 cm Tissue Culture dishes and allowed to recover overnight at 37 degrees and 5% CO2. In the am, supernatant was removed, and 12 mL of fresh medium with either 2.5 micromolar Compound C6 or a v/v match of DMSO (vehicle control) was added to the cells. Cells were incubated at 37 degrees in 5% CO2 for 30 minutes. Cells were washed 3X with cold DPBS++ and 10 mL of medium was added to the cells with either 1.0 micromolar Compound C6 or v/v match of DMSO. Cells were incubated at 37 degrees and 5% CO2 for 7.0 hours. Cells were washed with 10 mL of 150 mM Ammonium Acetate, swirled, washed again with 5 mL, and immediately quenched with liquid nitrogen. Cells were then frozen at -80 degrees.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
7
TOTAL_SUBJECTS
1
STUDY_COMMENTS
I request that the metabolites of the TCA+ assay that are to be assessed quantitatively please be sure to include ATP, ADP, AMP, NAD, NADH, NADP, NADPH, E4P, S7P, 6PG, G3P, H6P, and Lactate in particular. Also, I would request that both reduced and oxidized Glutathione as well as Fructose 1,6-bisphosphate be included in the non-quantitative data.
Pilot Human Muscle oral glucose tolerance test (OGTT)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Obesity is associated with metabolic inflexibility, the inability to switch from lipid to glucose oxidation during physiological conditions favoring excess glucose and insulin, which could contribute to the increased incidence of type 2 diabetes. Despite this knowledge, the role of skeletal muscle metabolites during these physiological conditions remain unclear and warrant further investigation. The purpose of this pilot study is to determine if: 1) there are differences in skeletal muscle glycolysis and TCA metabolites and amino acids between lean and obese individuals in the fasted state, and 2) if these metabolites change after 50 min of glucose ingestion, and 3) if there are differences in these metabolites between lean and obese individuals after 50 min of glucose ingestion.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
In the first group of samples, we are looking into the different metabolites and their concentrations within our human embryonic stem cells over the course of differentiation. Our goal is to study how the metabolism of stem cells are changing as they undergo this conversion to become hepatocyte-like cells. In the second group of samples labeled HyCell, we would like to understand the concentrations of metabolites within our CHO cells in order to update the parameters for our metabolic model. Included are two samples from different days of a suspension batch culture which may have different lactate production qualities.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Effect of cooling on muscle tissue metabolism (part II)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Thermal modalities are commonly used in sports medicine to affect tissue healing. Cold therapy is commonly used modalities, but the metabolic changes to muscle after cooling are not known. The objective of this study is to look at the effect of cooling on muscle metabolites and gene expression. There are a total of 8 subjects in the study. Each subject had an ice cup cryotherapy treatment ("cool" samples) to one leg for 15 minutes, and the other leg served as the control ("cntrl" samples). Two hours after the application of cryotherapy, a biopsy was taken from each thigh muscle. Muscle was minced with scissors and quickly snap frozen in liquid nitrogen.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
10
TOTAL_SUBJECTS
8
STUDY_COMMENTS
We would like to run the TCA Plus Analysis on each of the samples. For the statistical analysis, we would normalize the cool side to the ctrl side, and look at the relative change in metabolite abundance as a result of the cooling procedure. only used in sports medicine to affect tissue healing.
Diabetic heart adrenergic signaling and metabolism (STZ & Isoproterenol, High Fat)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
We are examing the effect of both diabetes and adrenergic activation on the metabolomic profile. STZ treatment was initiated 5 months before hearts were harvested. High fat/low fat diets were given for 13 weeks. All hearts were excised in the morning. For the STZ/isoproterenol experiment, mouse anesthesia was initiated with 4% isoflurane, and maintained with 2% and a homeothermic controller. After 5 min of equilibration, control and fasted mice were injected intraperitoneally with either saline (S) or 25ug/kg isoproterenol (I). After an additional 5 min, the whole heart was quickly excised, washed with ice-cold distilled water, dried off with a chem whipe, and flash frozen in liquid nitrogen. Hearts were stored at -80, and shipped using dry ice. The hearts from the high fat diet experiement were prepared in the same way, but no injection was given and total anesthesia time was 5min instead of 10min.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolomics of muscle in insulin sensitive and resistant obese indivduals.
STUDY_TYPE
MS analysis
STUDY_SUMMARY
"OC" samples: muscle biopsy samples collected from insulin sensitive / insulin resistant obese indivduals before undergoing a hyperinsulinemic-euglycemic clamp. Subjects were previously categorized for the rate of fatty acid release from adipose tissue into the bloodstream as a measure of insuline resistance. Low-FA, Med-FA, and High-FA stand for low, medium, and high rate of release.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Untargeted metabolomic profile of oak and wine yeast strains
STUDY_SUMMARY
Metabolomic profiles were compiled from oak and wine yeast parents over three extraction times (batch). Included in this study are extraction controls.
INSTITUTE
Washington University in St. Louis
LAST_NAME
Swain Lenz
FIRST_NAME
Devjanee
ADDRESS
4515 McKinley Avenue, Saint Louis, Missouri, 63110, USA
Metabolomic profiles were compiled from reciprocal hemizygotes (oak/win hybrid, genes AUA1, ARG82) (batch). Included in this study are extraction controls.
INSTITUTE
Washington University in St. Louis
LAST_NAME
Swain Lenz
FIRST_NAME
Devjanee
ADDRESS
4515 McKinley Avenue, Saint Louis, Missouri, 63110, USA
Maternal Hypoxemia and oxidative stress in the fetus, newborn, and adult. exercise training for peripheral artery disease
STUDY_TYPE
Disease model
STUDY_SUMMARY
Gestational hypoxia presents a significant stress to an unborn fetus that can lead to significant complications related to fetal growth restriction and resulting in diseases in the newborn as well as those manifesting later in life. Recent evidence indicates that inflammation and oxidative stress are contributing factors to hypoxia-related diseases. The Center for Perinatal Biology at Loma Linda University has studied gestational chronic hypoxia in a sheep model for over 20 years to study dysfunction of vascular and nonvascular tissues derived from mothers, fetuses and offspring. In this project we are attempting to use metabolomics to assess metabolic dysregulation in vascular tissues along with markers of oxidative stress and inflammation in the mother and offspring to determine the extent of dysregulation due to chronic hypoxia. Untargeted metabolomics analysis focused on sheep plasma and arteries from the lung, resistance arteries in the brain, uterine arteries, and cultured human myocytes will be used to explore markers of glucose and lipid metabolism disruption. Targeted analyses of oxylipins and endocannabinoids will be used on the same samples to explore markers of oxidative stress and inflammation, which should be increased during hypoxia. This study should delineate pathways and biomarkers that help explain how hypoxia leads to the development of neonatal as well as adult-onset diseases associated with chronic hypoxia that are inter-related with fetal growth restriction.
Maternal Hypoxemia and oxidative stress in the fetus, newborn, and adult. exercise training for peripheral artery disease (part II)
STUDY_TYPE
Disease model
STUDY_SUMMARY
Gestational hypoxia presents a significant stress to an unborn fetus that can lead to significant complications related to fetal growth restriction and resulting in diseases in the newborn as well as those manifesting later in life. Recent evidence indicates that inflammation and oxidative stress are contributing factors to hypoxia-related diseases. The Center for Perinatal Biology at Loma Linda University has studied gestational chronic hypoxia in a sheep model for over 20 years to study dysfunction of vascular and nonvascular tissues derived from mothers, fetuses and offspring. In this project we are attempting to use metabolomics to assess metabolic dysregulation in vascular tissues along with markers of oxidative stress and inflammation in the mother and offspring to determine the extent of dysregulation due to chronic hypoxia. Untargeted metabolomics analysis focused on sheep plasma and arteries from the lung, resistance arteries in the brain, uterine arteries, and cultured human myocytes will be used to explore markers of glucose and lipid metabolism disruption. Targeted analyses of oxylipins and endocannabinoids will be used on the same samples to explore markers of oxidative stress and inflammation, which should be increased during hypoxia. This study should delineate pathways and biomarkers that help explain how hypoxia leads to the development of neonatal as well as adult-onset diseases associated with chronic hypoxia that are inter-related with fetal growth restriction.
Fatty Acid Oxidation is Impaired in An Orthologous Mouse Model of Autosomal Dominant Polycystic Kidney Disease
STUDY_SUMMARY
Autosomal Dominant Polycystic Kidney Disease (ADPKD; MIM ID's 173900, 601313, 613095) is estimated to affect almost 1/1000 and is the most common genetic cause of end stage renal disease (Torres et al., 2007). While advances have been made in slowing the progression of some other forms of chronic kidney disease, standard treatments have not reduced the need for renal replacement therapy in ADPKD (Spithoven et al., 2014). Unfortunately, several experimental interventions also have recently failed to show significant benefit in slowing the rate of functional decline (Serra et al., 2010; Walz et al., 2010; Schrier et al., 2014; Torres et al., 2014), and the only positive study reported very modest effects (Torres et al., 2012). These findings suggest new treatment strategies are required. A central dogma of molecular genetics is that discovery of the causative genes will lead to identification of key pathways and potential targets for intervention. In the case of ADPKD, the two genes mutated in the disorder, PKD1 and PKD2, were identified almost 20 years ago and yet their functions remain poorly understood. The PKD1 gene product, polycystin-1 (PC1), encodes a large membrane protein that requires the PKD2 gene product, polycystin-2 (PC2), for its trafficking to the primary cilium where the two are thought to form a receptor channel complex (Kim et al., 2014; Cai et al., 2014). What the complex senses and what it signals remains controversial. The primary cilium has emerged as a key player in the pathogenesis of PKD as mutations in dozens of different genes that encode either essential ciliary components or factors in ciliary signaling pathways result in PKD. A recent report suggests that the relationship between the polycystin complex and ciliary signaling is complicated, however.While ablation of primary cilia by mutation of core ciliary components results in cysts, these same perturbations done in the setting of Pkd1 or Pkd2 inactivation results in significant attenuation of cystic disease (Ma et al., 2013). These data suggest that the polycystin complex provides a suppressive signal for a novel, cilia-dependent growth-promoting pathway that is independent of MAPK/ERK, mTOR, or cAMP pathways, three effector pathways previously implicated as major drivers of cyst growth. The identities of the growth-promoting and growth-inhibiting pathways remain unknown. We have taken a systems-based approach to study Pkd1 gene function. Building on our previous work identifying markedly different outcomes in animals with induced Pkd1 inactivation before or after P12 and correlating this susceptibility with metabolic status (Piontek et al., 2007; Menezes et al., 2012), we now show that female sex is partially protective in adult-induced Pkd1 inactivation, that sex differences in metabolic status may account for this effect, and that cells lacking Pkd1 have abnormal fatty acid oxidation. Finally, manipulating diet in Pkd1 mouse models, we demonstrate a positive correlation between lipid content in mouse chow and cystic kidney disease severity. Our results therefore suggest that abnormal lipid metabolism is an intrinsic component of PKD and an important modifier of disease progression.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Diet, genetics and gut microbiome drive dynamic changes in plasma metabolites [plasma]
STUDY_TYPE
Plasma data
STUDY_SUMMARY
C57BL/6J mice (B6) and 129S1 mice (129J) were purchased from Jackson Laboratory (Bar Harbor, ME) and 129S6 mice (129T) were purchased from Taconic Farms (Germantown, NY). Mice were maintained on normal chow containing 22% calories from fat, 23% from protein and 55% from carbohydrates (Mouse Diet 9F 5020, PharmaServ, Framingham, MA) or a high fat diet (Open Source Diet, D12492, Research Diets, New Brunswick, NJ) containing 60% calories from fat, 20% from protein and 20% from carbohydrates. For antibiotic treatment, 6-week old mice were treated with either placebo, vancomycin (1g/L) or metronidazole (1g/L) (Sigma-Aldrich, St. Louis, MO) in drinking water then started on HFD from age 7 to 11 weeks. The mice were fasted for 2 hours and anesthetized with isoflurane before collecting cecum and plasma.
Diet, genetics and gut microbiome drive dynamic changes in plasma metabolites [cecal]
STUDY_TYPE
Cecal data
STUDY_SUMMARY
C57BL/6J mice (B6) and 129S1 mice (129J) were purchased from Jackson Laboratory (Bar Harbor, ME) and 129S6 mice (129T) were purchased from Taconic Farms (Germantown, NY). Mice were maintained on normal chow containing 22% calories from fat, 23% from protein and 55% from carbohydrates (Mouse Diet 9F 5020, PharmaServ, Framingham, MA) or a high fat diet (Open Source Diet, D12492, Research Diets, New Brunswick, NJ) containing 60% calories from fat, 20% from protein and 20% from carbohydrates. For antibiotic treatment, 6-week old mice were treated with either placebo, vancomycin (1g/L) or metronidazole (1g/L) (Sigma-Aldrich, St. Louis, MO) in drinking water then started on HFD from age 7 to 11 weeks. The mice were fasted for 2 hours and anesthetized with isoflurane before collecting cecum and plasma.
Breathprinting Reveals Malaria-Associated Biomarkers and Mosquito Attractants
STUDY_SUMMARY
Current evidence suggests that malaria infection could alter patient breath metabolites, a phenomenon that could be exploited to create a breath-based diagnostic test. Indications include the preferential attraction of the Anopheles mosquito vector upon infection and a distinct breath profile with the progression of experimental, sub-microscopic malaria. However, these observations have yet to be extended to the clinic. To investigate whether natural human malaria infection leads to a characteristic breath profile, we performed a field study in Malawi. Breath volatiles from pediatric patients with and without uncomplicated falciparum malaria were analyzed by thermal desorption-gas chromatography/mass spectrometry. Using an unbiased, correlation-based analysis, we find that children with malaria have a distinct shift in overall breath composition. Leveraging these differences, highly accurate classification of infection status was achieved with a suite of six compounds. In addition, we find that malaria-infected children have significantly higher breath levels of two mosquito-attractant terpenes, α-pinene and 3-carene. Thus, our work attests to the viability of breath analysis for malaria diagnosis, identifies candidate compounds for follow-up studies, and identifies biologically plausible chemical mediators for increased mosquito attraction to malaria-infected patients.
INSTITUTE
Washington University School of Medicine
LAST_NAME
Schaber
FIRST_NAME
Chad
ADDRESS
4938 Parkview Place, MPRB/FLoor 6, Entry 5, St. Louis, MO, 63110, USA
Gut Microbiota Modulate Brain Insulin Sensitivity and Neurobehavior
STUDY_TYPE
Metabolite profiling of cecal contents and brains of mice under diet-induced obesity (DIO) with and without antibiotic treatments.
STUDY_SUMMARY
C57BL/6J mice were purchased from Jackson Laboratory and maintained on either a normal chow containing 22% of calories from fat, 23% from protein, and 55% from carbohydrates (Mouse diet 9F 5020; PharmaServ) or a high-fat diet (Open Source Diet, D12492; Research Diets) containing 60% of calories from fat, 20% from protein, and 20% from carbohydrates for 6 weeks. During the last 2 weeks, some of the HFD mice were treated with vancomycin or metronidazole (1 g/L in the drinking water). All mice were housed at 22°C on a 12 h light/dark cycle. All animal studies were approved by the IACUC of Joslin Diabetes Center (# 97-05) and Harvard Medical School (# 05131) and were in accordance with NIH guidelines. The metabolite profiling was conducted on plasma, hypothalamus and nucleus accumbens.
Retrospective serum samples from patients with early Lyme disease, other diseases, and healthy controls were analyzed for small molecule metabolites by liquid chromatography-mass spectrometry (LC-MS). A metabolomics data workflow was applied to select a biosignature for classifying early Lyme disease and non-Lyme disease patients. A statistical model of the biosignature was trained using the patients' LC-MS data, and subsequently applied as an experimental diagnostic tool with LC-MS data from additional patient sera.
INSTITUTE
Colorado State University
DEPARTMENT
MIP
LABORATORY
Belisle
LAST_NAME
Belisle
FIRST_NAME
John
ADDRESS
200 West Lake, Campus Delivery 0922, Colorado State University, Fort Collins, CO, 80523, USA
EMAIL
john.belisle@colostate.edu
PHONE
970-491-5384
NUM_GROUPS
9
STUDY_COMMENTS
All samples and data used in training are provided. All samples and data used in testing are provided, except healthy controls that were experimentally heat treated.
GC-MS analysis of Quercus ilex organs (leaves, roots and acorns)
STUDY_TYPE
Untargeted metabolomics
STUDY_SUMMARY
Qualitative metabolomics study on leaves, roots and acorns from Quercus ilex plantlets. We analyzed polar(metanol:water) and apolar (chloroform) fractions.
INSTITUTE
Universidad de Córdoba
DEPARTMENT
Department Biochemistry and Molecular Biology
LABORATORY
Agroforestry and Plant Biochemistry, Proteomics and Systems Biology
Analysis of the effects of Tyrosine Kinase Inhibitors Sunitinib and Erlotinib on Heart, Metabolism In Vivo
STUDY_SUMMARY
Background.More than 90 tyrosine kinases have been implicated in the pathogenesis of malignant transformation and tumor angiogenesis. Tyrosine kinase inhibitors (TKIs) have emerged as effective therapies in treating cancer by exploiting this kinase dependency. The tyrosine kinase inhibitor erlotinib targets epidermal growth factor receptor (EGFR), whereas sunitinib targets primarily vascular endothelial growth factor receptor (VEGRF) and platelet-derived growth factor receptor (PDGFR). TKIs impact the function of non-malignant cells had have on- and off-target toxicities, including cardiotoxicities. Most of the reports of sunitinib have identified cardiotoxic effects, whereas erlotinib was less often found to have these effects. We hypothesized that the deleterious effects of TKIs were related to their impact on cardiac metabolism. Methods. C57BL/6 mice (10/group) were treated with therapeutic doses of sunitinib (40 mg/kg), erlotinib (50 mg/kg), or vehicle daily for 2 weeks. Echocardiographic assessment of the heart in vivo identified significant systolic dysfunction consistent with cardiotoxicity compared to vehicle treated controls. Heart, skeletal muscle, liver, and serum were flash frozen and prepped for non-targeted GC-MS metabolomics analysis. Results. Compared to vehicle treated controls, sunitinib treated mice had significant decreases insystolic function, whereas erlotinib treated mice did not. Non-Targeted metabolomics analysis of heart identified identified significant decreases in Docosahexaenoic acid (DHA), Arachidonic Acid/Eicosapentaenoic acid (EPA), O-Phosphocolamine, and 6-Hydroxynicotinic acid after sunitinib treatment. DHA was significantly decreased in skeletal muscle (quadriceps femoris), with elevations in cholesterol were identified in liver and elevated ethanol amine in serum. In contrast, erlotinib affected only one metabolite elevated (spermidine significantly increased).Conclusions.Mice treated with sunitinib had exhibited systolic dysfunction within two weeks, with significantly lower heart and skeletal muscle levels of long chain omega-3 fatty acids docosahexaenoic acid (DHA), arachidonic acid (AA)/eicosapentaenoic acid (EPA) and increased serum O-Phosphocholine phospholipid. This is the first link between sunitinib-induced cardiotoxicity and depletion in the polyunsaturated fatty acids (PUFAs) and inflammatory mediators DHA and AA/EPA in the heart, possibly by affecting mitochondria function where they have vital roles on calcium channels.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister heart Institute, Department of Internal medicine
LABORATORY
Multiple Centers
LAST_NAME
Willis
FIRST_NAME
Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
EMAIL
monte_willis@med.unc.edu
PHONE
919-360-7599
STUDY_COMMENTS
Cardiac tissue, Gastrocnemius Muscle, Liver, and Serum
Analysis of the effects of Tyrosine Kinase Inhibitors Sunitinib and Erlotinib on Liver Metabolism In Vivo
STUDY_SUMMARY
Background.More than 90 tyrosine kinases have been implicated in the pathogenesis of malignant transformation and tumor angiogenesis. Tyrosine kinase inhibitors (TKIs) have emerged as effective therapies in treating cancer by exploiting this kinase dependency. The tyrosine kinase inhibitor erlotinib targets epidermal growth factor receptor (EGFR), whereas sunitinib targets primarily vascular endothelial growth factor receptor (VEGRF) and platelet-derived growth factor receptor (PDGFR). TKIs impact the function of non-malignant cells had have on- and off-target toxicities, including cardiotoxicities. Most of the reports of sunitinib have identified cardiotoxic effects, whereas erlotinib was less often found to have these effects. We hypothesized that the deleterious effects of TKIs were related to their impact on cardiac metabolism. Methods. C57BL/6 mice (10/group) were treated with therapeutic doses of sunitinib (40 mg/kg), erlotinib (50 mg/kg), or vehicle daily for 2 weeks. Echocardiographic assessment of the heart in vivo identified significant systolic dysfunction consistent with cardiotoxicity compared to vehicle treated controls. Heart, skeletal muscle, liver, and serum were flash frozen and prepped for non-targeted GC-MS metabolomics analysis. Results. Compared to vehicle treated controls, sunitinib treated mice had significant decreases insystolic function, whereas erlotinib treated mice did not. Non-Targeted metabolomics analysis of heart identified identified significant decreases in Docosahexaenoic acid (DHA), Arachidonic Acid/Eicosapentaenoic acid (EPA), O-Phosphocolamine, and 6-Hydroxynicotinic acid after sunitinib treatment. DHA was significantly decreased in skeletal muscle (quadriceps femoris), with elevations in cholesterol were identified in liver and elevated ethanol amine in serum. In contrast, erlotinib affected only one metabolite elevated (spermidine significantly increased).Conclusions.Mice treated with sunitinib had exhibited systolic dysfunction within two weeks, with significantly lower heart and skeletal muscle levels of long chain omega-3 fatty acids docosahexaenoic acid (DHA), arachidonic acid (AA)/eicosapentaenoic acid (EPA) and increased serum O-Phosphocholine phospholipid. This is the first link between sunitinib-induced cardiotoxicity and depletion in the polyunsaturated fatty acids (PUFAs) and inflammatory mediators DHA and AA/EPA in the heart, possibly by affecting mitochondria function where they have vital roles on calcium channels.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister heart Institute, Department of Internal medicine
LABORATORY
Multiple Centers
LAST_NAME
Willis
FIRST_NAME
Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
EMAIL
monte_willis@med.unc.edu
PHONE
919-360-7599
STUDY_COMMENTS
Cardiac tissue, Gastrocnemius Muscle, Liver, and Serum
Analysis of the effects of Tyrosine Kinase Inhibitors Sunitinib and Erlotinib on Serum Metabolism In Vivo using Non-Targeted Metabolomics Analysis
STUDY_SUMMARY
Background.More than 90 tyrosine kinases have been implicated in the pathogenesis of malignant transformation and tumor angiogenesis. Tyrosine kinase inhibitors (TKIs) have emerged as effective therapies in treating cancer by exploiting this kinase dependency. The tyrosine kinase inhibitor erlotinib targets epidermal growth factor receptor (EGFR), whereas sunitinib targets primarily vascular endothelial growth factor receptor (VEGRF) and platelet-derived growth factor receptor (PDGFR). TKIs impact the function of non-malignant cells had have on- and off-target toxicities, including cardiotoxicities. Most of the reports of sunitinib have identified cardiotoxic effects, whereas erlotinib was less often found to have these effects. We hypothesized that the deleterious effects of TKIs were related to their impact on cardiac metabolism. Methods. C57BL/6 mice (10/group) were treated with therapeutic doses of sunitinib (40 mg/kg), erlotinib (50 mg/kg), or vehicle daily for 2 weeks. Echocardiographic assessment of the heart in vivo identified significant systolic dysfunction consistent with cardiotoxicity compared to vehicle treated controls. Heart, skeletal muscle, liver, and serum were flash frozen and prepped for non-targeted GC-MS metabolomics analysis. Results. Compared to vehicle treated controls, sunitinib treated mice had significant decreases insystolic function, whereas erlotinib treated mice did not. Non-Targeted metabolomics analysis of heart identified identified significant decreases in Docosahexaenoic acid (DHA), Arachidonic Acid/Eicosapentaenoic acid (EPA), O-Phosphocolamine, and 6-Hydroxynicotinic acid after sunitinib treatment. DHA was significantly decreased in skeletal muscle (quadriceps femoris), with elevations in cholesterol were identified in liver and elevated ethanol amine in serum. In contrast, erlotinib affected only one metabolite elevated (spermidine significantly increased).Conclusions.Mice treated with sunitinib had exhibited systolic dysfunction within two weeks, with significantly lower heart and skeletal muscle levels of long chain omega-3 fatty acids docosahexaenoic acid (DHA), arachidonic acid (AA)/eicosapentaenoic acid (EPA) and increased serum O-Phosphocholine phospholipid. This is the first link between sunitinib-induced cardiotoxicity and depletion in the polyunsaturated fatty acids (PUFAs) and inflammatory mediators DHA and AA/EPA in the heart, possibly by affecting mitochondria function where they have vital roles on calcium channels.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister heart Institute, Department of Internal medicine
LABORATORY
Multiple Centers
LAST_NAME
Willis
FIRST_NAME
Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
EMAIL
monte_willis@med.unc.edu
PHONE
919-360-7599
STUDY_COMMENTS
Cardiac tissue, Gastrocnemius Muscle, Liver, and Serum
Analysis of the effects of Tyrosine Kinase Inhibitors Sunitinib and Erlotinib on Muscle Metabolism In Vivo
STUDY_SUMMARY
Background.More than 90 tyrosine kinases have been implicated in the pathogenesis of malignant transformation and tumor angiogenesis. Tyrosine kinase inhibitors (TKIs) have emerged as effective therapies in treating cancer by exploiting this kinase dependency. The tyrosine kinase inhibitor erlotinib targets epidermal growth factor receptor (EGFR), whereas sunitinib targets primarily vascular endothelial growth factor receptor (VEGRF) and platelet-derived growth factor receptor (PDGFR). TKIs impact the function of non-malignant cells had have on- and off-target toxicities, including cardiotoxicities. Most of the reports of sunitinib have identified cardiotoxic effects, whereas erlotinib was less often found to have these effects. We hypothesized that the deleterious effects of TKIs were related to their impact on cardiac metabolism. Methods. C57BL/6 mice (10/group) were treated with therapeutic doses of sunitinib (40 mg/kg), erlotinib (50 mg/kg), or vehicle daily for 2 weeks. Echocardiographic assessment of the heart in vivo identified significant systolic dysfunction consistent with cardiotoxicity compared to vehicle treated controls. Heart, skeletal muscle, liver, and serum were flash frozen and prepped for non-targeted GC-MS metabolomics analysis. Results. Compared to vehicle treated controls, sunitinib treated mice had significant decreases insystolic function, whereas erlotinib treated mice did not. Non-Targeted metabolomics analysis of heart identified identified significant decreases in Docosahexaenoic acid (DHA), Arachidonic Acid/Eicosapentaenoic acid (EPA), O-Phosphocolamine, and 6-Hydroxynicotinic acid after sunitinib treatment. DHA was significantly decreased in skeletal muscle (quadriceps femoris), with elevations in cholesterol were identified in liver and elevated ethanol amine in serum. In contrast, erlotinib affected only one metabolite elevated (spermidine significantly increased).Conclusions.Mice treated with sunitinib had exhibited systolic dysfunction within two weeks, with significantly lower heart and skeletal muscle levels of long chain omega-3 fatty acids docosahexaenoic acid (DHA), arachidonic acid (AA)/eicosapentaenoic acid (EPA) and increased serum O-Phosphocholine phospholipid. This is the first link between sunitinib-induced cardiotoxicity and depletion in the polyunsaturated fatty acids (PUFAs) and inflammatory mediators DHA and AA/EPA in the heart, possibly by affecting mitochondria function where they have vital roles on calcium channels.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister heart Institute, Department of Internal medicine
LABORATORY
Multiple Centers
LAST_NAME
Willis
FIRST_NAME
Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
EMAIL
monte_willis@med.unc.edu
PHONE
919-360-7599
STUDY_COMMENTS
Cardiac tissue, Gastrocnemius Muscle, Liver, and Serum
Untargeted metabolomics analysis of ischemia-reperfusion injured hearts ex vivo from sedentary and exercise trained rats.
STUDY_SUMMARY
The effects of exercise on the heart and its resistance to disease are well-documented. Recent studies have identified exercise-induced resistance to arrhythmia is due to the preservation of mitochondrial membrane potential. To identify novel metabolic changes that occurred parallel to these mitochondrial alterations, we performed non-targeted metabolomics analysis on hearts from sedentary (Sed) and exercise- trained (Ex) rats challenged with isolated heart ischemia-reperfusion injury (I/R). Eight weeks old Sprague- Dawley rats were treadmill trained five days/week for six weeks (exercise duration and intensity progressively increased to 1 hour at 30 m/min up to 10.5% incline, 75-80% VO2mx). The recovery of pre-ischemic function for sedentary rat hearts was 28.8+/-5.4% (N=12) compared to exercise trained hearts which recovered 51.9%+/-5.7 (N=14)(p<0.001). Non-targeted GC-MS metabolomics analysis of 1) Sedentary rat hearts; 2) Exercise-trained rat hearts; 3) Sedentary rat hearts challenged with global ischemia-reperfusion (I/R) injury; and 4) Exercise-trained rat hearts challeged with global I/R (10/group) revealed 20 statistically significant metabolites between groups by ANOVA using Metaboanalyst (p<0.001). Enrichment analysis of these metabolites for pathway-associated metabolic sets indicated a >10 fold enrichment for ammonia recycling and protein biosynthesis (L-Glutamic acid; L-Proline; L-Histidine; L-Serine; L-Aspartic acid; L-Glutamine)(p<=4.05E-05, FDR=0.0024). Subsequent comparison of the sedentary hearts post-I/R and exercise-trained hearts post-I/R further identified significant differences in metabolites related to Aminoacyl-tRNA biosynthesis and nitrogen metabolism (4) (p<=1.24E-05, FDR<=5.07E-4). These studies shed light on novel mechanisms in which exercise-induced cardioprotection occurs in I/R which complement both the mitochondrial stabilization and antioxidant mechanisms recently described. These findings also link protein synthesis and protein degradation (protein quality control mechanisms) with exercise-linked cardioprotection and mitochondrial susceptibility for the first time in cardiac I/R.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister heart Institute, Department of Internal medicine
LABORATORY
Multiple Centers
LAST_NAME
Willis
FIRST_NAME
Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
TAp73 is a marker of glutamine addiction in medulloblastoma
STUDY_TYPE
siRNA constructs targeting p73 (ID: 2671-AMBION) and a non-targeting control siRNA (scramble) were transfected with 10 pM siRNA with lipofectamine 3000 according to the supplier’s protocol for 48 hours
STUDY_SUMMARY
Metabolically-targeted therapies hold the promise of offering an effective and less toxic treatment for tumours including medulloblastoma, the most common malignant brain tumour of childhood. Current treatment relies on the sensitivity of these tumours to DNA damage that was discovered more than 50 years ago. Finding new tumour-specific susceptibilities to complement sensitivity to DNA damage is key to developing new more effective adjuvant therapies. The specific metabolic program of tumours is an attractive vulnerability, as restriction diet are low cost and easy to implement. Here, we present compelling pre-clinical evidence that glutamine restriction diet can be used as an adjuvant treatment for p73-expressing medulloblastoma.
INSTITUTE
Queen Mary University of London
DEPARTMENT
Blizard Institute
LABORATORY
Centre for Genomics and Child Health
LAST_NAME
Marino
FIRST_NAME
Silvia
ADDRESS
4 Newark Street, E1 2AT, London
EMAIL
s.marino@qmul.ac.uk
PHONE
+44 20 7882 2360
NUM_GROUPS
2
TOTAL_SUBJECTS
18
STUDY_COMMENTS
We include 3 biological replicate with 3 technical replicates for each condition.
Alterations in Lipid, Amino Acid, and Energy Metabolism Distinguish Crohn Disease from Ulcerative Colitis and Control Subjects by Serum Metabolomic Profiling
STUDY_SUMMARY
Non-invasive biomarkers are needed in inflammatory bowel disease (IBD) to help define disease activity and identify underlying pathogenic mechanisms. We hypothesized that serum metabolomics, which produces unique metabolite profiles, can aid in this search. The aim of this study was to characterize serum metabolomic profiles in patients with IBD, and to assess for differences between patients with ulcerative colitis (UC), Crohn disease (CD), and non-IBD subjects. Serum samples from 20 UC, 20 CD, and 20 non-IBD control subjects were obtained along with patient characteristics, including medication use and clinical disease activity. Non-targeted metabolomic profiling was performed using ultra-high performance liquid chromatography/mass spectrometry (UPLC-MS/MS) optimized for basic or acidic species and hydrophilic interaction liquid chromatography (HILIC/UPLC-MS/MS).
INSTITUTE
Vanderbilt University Medical Center
LAST_NAME
Elizabeth
FIRST_NAME
Scoville
ADDRESS
1030C MRB IV, 2215 Garland Avenue, Nashville, TN, 37232, USA
Evidence that the metabolite repair enzyme NAD(P)HX epimerase has a moonlighting function
STUDY_SUMMARY
NAD(P)H-hydrate epimerase (EC 5.1.99.6) is known to help repair NAD(P)H hydrates (NAD(P)HX), which are damage products existing as R and S epimers. The S epimer is reconverted to NAD(P)H by a dehydratase; the epimerase facilitates epimer interconversion. Epimerase deficiency in humans causes a lethal disorder attributed to NADHX accumulation. However, bioinformatic evidence suggests caution about this attribution by predicting that the epimerase has a second function connected to vitamin B6 (pyridoxal 5'-phosphate and related compounds). Specifically, (i) the epimerase is fused to a B6 salvage enzyme in plants, (ii) epimerase genes cluster on the chromosome with B6-related genes in bacteria, and (iii) epimerase and B6-related genes are coexpressed in yeast and Arabidopsis. The predicted second function was explored in Escherichia coli, whose epimerase and dehydratase are fused and encoded by the yjeF gene. The putative NAD(P)HX epimerase active site has a conserved lysine residue (K192 in E. coli YjeF). Changing this residue to alanine cut in-vitro epimerase activity by ≥95% but did not affect dehydratase activity. Mutant cells carrying the K192A mutation had essentially normal NAD(P)HX levels, showing that the mutation had very little or no effect on NAD(P)HX repair in vivo. However, these cells showed metabolome changes, particularly in amino acids, that exceeded those in cells lacking the entire yjeF gene. The K192A mutant cells also had lower levels of free pyridoxal 5'-phosphate than wild-type cells. These results provide strong circumstantial evidence that the epimerase has a metabolic function beyond NAD(P)HX repair and that this function involves vitamin B6.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Pharmacometabolomic analysis of rat hippocampus and plasma in response to chronic stress and albiflorin treament
STUDY_TYPE
Animal study
STUDY_SUMMARY
Male Sprague-Dawley (SD) rats were exposed to one random stressor per day for 35 d. Following four weeks of stress exposure, rats with stress-induced depression-like behaviors were treated daily with either saline, fluoxetine or albiflorin for 7 days via intragastric gavage. Rat heparinized plasma was collected after drug treatment. After behavior tests, rats were sacrificed and the hippocampus was collected. Pharmacometabolomic analysis was conducted for both plasma and hippocampal samples
INSTITUTE
Beijing Woner Biotech Co. Ltd
LAST_NAME
Zhang
FIRST_NAME
Zuoguang
ADDRESS
No.9, Kexing Road, Fengtai, Beijing, Beijing, 101111, China
Insights into the pathogenesis of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) through metabolomic profiling of cerebrospinal fluid (part I)
STUDY_SUMMARY
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a disabling illness characterized by six months or more of unexplained profound fatigue with post-exertional malaise, sleep abnormalities, cognitive dysfunction and autonomic disturbances. Focusing on the pathogenesis of central nervous system abnormalities in ME/CFS, we pursued metabolomics analysis of cerebrospinal fluid (CSF) in 32 ME/CFS cases, 40 subjects with multiple sclerosis (MS), another fatiguing illness, and 19 healthy subjects with no neurological disease (ND). MS/ND subjects were frequency matched for age and sex to ME/CFS subjects. Three untargeted metabolomic assays for primary metabolites, biogenic amines and complex lipids were performed with gas chromatography time-of-flight (GC-TOF) and liquid chromatography–tandem mass spectrometry (LC-MS/MS) yielding profiles for 525 known metabolites. Mannose was a cardinal biomarker in ME/CFS subjects with reduced levels in ME/CFS compared to both MS and ND subjects. Levels of acetylcarnitine were reduced in ME/CFS vs. MS subjects. The predictive power of metabolomic analysis for diagnosis of ME/CFS vs. ND was higher (cross-validated AUC 0.875; 95% CI: 0.726~0.949) than with cytokine analysis alone (cross-validated AUC 0.865; 95% CI: 0.673~0.952) and improved with integration of both metabolomics and cytokine analyses (cross-validated AUC 0.916; 95% CI: 0.791~0.969). Our findings confirm the biological basis of ME/CFS, and may enable new methods for diagnosis and insight into cognitive and autonomic disturbances in this syndrome.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Insights into the pathogenesis of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) through metabolomic profiling of cerebrospinal fluid (part II)
STUDY_SUMMARY
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a disabling illness characterized by six months or more of unexplained profound fatigue with post-exertional malaise, sleep abnormalities, cognitive dysfunction and autonomic disturbances. Focusing on the pathogenesis of central nervous system abnormalities in ME/CFS, we pursued metabolomics analysis of cerebrospinal fluid (CSF) in 32 ME/CFS cases, 40 subjects with multiple sclerosis (MS), another fatiguing illness, and 19 healthy subjects with no neurological disease (ND). MS/ND subjects were frequency matched for age and sex to ME/CFS subjects. Three untargeted metabolomic assays for primary metabolites, biogenic amines and complex lipids were performed with gas chromatography time-of-flight (GC-TOF) and liquid chromatography–tandem mass spectrometry (LC-MS/MS) yielding profiles for 525 known metabolites. Mannose was a cardinal biomarker in ME/CFS subjects with reduced levels in ME/CFS compared to both MS and ND subjects. Levels of acetylcarnitine were reduced in ME/CFS vs. MS subjects. The predictive power of metabolomic analysis for diagnosis of ME/CFS vs. ND was higher (cross-validated AUC 0.875; 95% CI: 0.726~0.949) than with cytokine analysis alone (cross-validated AUC 0.865; 95% CI: 0.673~0.952) and improved with integration of both metabolomics and cytokine analyses (cross-validated AUC 0.916; 95% CI: 0.791~0.969). Our findings confirm the biological basis of ME/CFS, and may enable new methods for diagnosis and insight into cognitive and autonomic disturbances in this syndrome.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Insights into the pathogenesis of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) through metabolomic profiling of cerebrospinal fluid
STUDY_SUMMARY
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a disabling illness characterized by six months or more of unexplained profound fatigue with post-exertional malaise, sleep abnormalities, cognitive dysfunction and autonomic disturbances. Focusing on the pathogenesis of central nervous system abnormalities in ME/CFS, we pursued metabolomics analysis of cerebrospinal fluid (CSF) in 32 ME/CFS cases, 40 subjects with multiple sclerosis (MS), another fatiguing illness, and 19 healthy subjects with no neurological disease (ND). MS/ND subjects were frequency matched for age and sex to ME/CFS subjects. Three untargeted metabolomic assays for primary metabolites, biogenic amines and complex lipids were performed with gas chromatography time-of-flight (GC-TOF) and liquid chromatography–tandem mass spectrometry (LC-MS/MS) yielding profiles for 525 known metabolites. Mannose was a cardinal biomarker in ME/CFS subjects with reduced levels in ME/CFS compared to both MS and ND subjects. Levels of acetylcarnitine were reduced in ME/CFS vs. MS subjects. The predictive power of metabolomic analysis for diagnosis of ME/CFS vs. ND was higher (cross-validated AUC 0.875; 95% CI: 0.726~0.949) than with cytokine analysis alone (cross-validated AUC 0.865; 95% CI: 0.673~0.952) and improved with integration of both metabolomics and cytokine analyses (cross-validated AUC 0.916; 95% CI: 0.791~0.969). Our findings confirm the biological basis of ME/CFS, and may enable new methods for diagnosis and insight into cognitive and autonomic disturbances in this syndrome.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Insights into the pathogenesis of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) through metabolomic profiling of cerebrospinal fluid
STUDY_SUMMARY
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a disabling illness characterized by six months or more of unexplained profound fatigue with post-exertional malaise, sleep abnormalities, cognitive dysfunction and autonomic disturbances. Focusing on the pathogenesis of central nervous system abnormalities in ME/CFS, we pursued metabolomics analysis of cerebrospinal fluid (CSF) in 32 ME/CFS cases, 40 subjects with multiple sclerosis (MS), another fatiguing illness, and 19 healthy subjects with no neurological disease (ND). MS/ND subjects were frequency matched for age and sex to ME/CFS subjects. Three untargeted metabolomic assays for primary metabolites, biogenic amines and complex lipids were performed with gas chromatography time-of-flight (GC-TOF) and liquid chromatography–tandem mass spectrometry (LC-MS/MS) yielding profiles for 525 known metabolites. Mannose was a cardinal biomarker in ME/CFS subjects with reduced levels in ME/CFS compared to both MS and ND subjects. Levels of acetylcarnitine were reduced in ME/CFS vs. MS subjects. The predictive power of metabolomic analysis for diagnosis of ME/CFS vs. ND was higher (cross-validated AUC 0.875; 95% CI: 0.726~0.949) than with cytokine analysis alone (cross-validated AUC 0.865; 95% CI: 0.673~0.952) and improved with integration of both metabolomics and cytokine analyses (cross-validated AUC 0.916; 95% CI: 0.791~0.969). Our findings confirm the biological basis of ME/CFS, and may enable new methods for diagnosis and insight into cognitive and autonomic disturbances in this syndrome.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Breast cancer is a highly heterogeneous disease associated with metabolic reprogramming. The shifts in the metabolome caused by breast cancer still lack data from Latin populations of Hispanic origin. In this pilot study, metabolomic and lipidomic approaches were performed to establish a plasma metabolic fingerprint of Colombian Hispanic women with breast cancer. NMR, GC-MS and LC-MS datasets were combined and compared. Statistics showed discrimination between breast cancer and healthy subjects on all analytical platforms.
Discovery of Lipidome Alterations Following Traumatic Brain Injury via High-Resolution Metabolomics
STUDY_TYPE
Untargeted lipidomics
STUDY_SUMMARY
Traumatic brain injury (TBI) can occur across wide segments of the population, presenting in a heterogeneous manner that makes diagnosis inconsistent and management challenging. Biomarkers offer the potential to objectively identify injury status, severity, and phenotype by measuring the relative concentrations of endogenous molecules in readily accessible biofluids. Through a data-driven, discovery approach, novel biomarker candidates for TBI were identified in the serum lipidome of adult male Sprague-Dawley rats in the first week following moderate controlled cortical impact (CCI). Serum samples were analyzed in positive and negative ion modes by Ultra Performance Liquid Chromatography Mass Spectrometry (UPLC-MS). A predictive panel for the classification of injured and uninjured sera samples, consisting of 26 dysregulated species belonging to a variety of lipid classes, was developed with a cross-validated accuracy of 85.3% using omniClassifier software to optimize feature selection,. Polyunsaturated fatty acids (PUFAs) and PUFA-containing diacylglycerols were found to be upregulated in sera from injured rats, while changes in sphingolipids and other membrane phospholipids were also observed, many of which map to known secondary injury pathways. Overall, the identified biomarker panel offers viable molecular candidates representing lipids that may readily cross the blood brain barrier (BBB) and aid in the understanding of TBI pathophysiology.
Karenia brevis allelopathy compromises the lipidome, membrane integrity, and photosynthetic efficiency of competitors
STUDY_TYPE
Untargeted lipidomics
STUDY_SUMMARY
Allelopathy, or the release of compounds that inhibit competitors, is a form of interference competition that is common among bloom-forming phytoplankton. Allelopathy is hypothesized to play a role in bloom propagation and maintenance and is well established in the red tide dinoflagellate Karenia brevis. K. brevis typically suppresses competitor growth through unknown mechanisms over the course of many days. When we investigated the effects of allelopathy on the lipidomes of two competing phytoplankton, Asterionellopsis glacialis and Thalassiosira pseudonana using nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS)- based metabolomics, we found that the lipidomes of both species were significantly altered, however A. glacialis maintained a more robust response whereas T. pseudonana saw significant alterations in fatty acid synthesis, cell membrane integrity, and a decrease in photosynthetic efficiency. Membrane- associated lipids were significantly suppressed for T. pseudonana exposed to allelopathy to the point of permeabilizing the cell membrane of living cells. The dominant mechanisms of K. brevis allelopathy appear to target lipid biosynthesis affecting multiple physiological pathways suggesting that exuded compounds have the ability to significantly alter competitor physiology and give K. brevis a competitive edge over sensitive species.
Longitudinal Metabolomics of the Human Microbiome in Inflammatory Bowel Disease
STUDY_SUMMARY
A number of factors contribute to the complex array of small molecules that occur in stool; including diet, gut flora, and gut function. Comprehensive profiling of the stool metabolome therefore can provide detailed phenotypic information on health status, metabolic interactions between the host and the microbiome, and interactions among gut microbes. Here, we applied metabolomics to characterize stool samples collected longitudinally from inflammatory bowel disease (IBD) patients and non-IBD controls who participated in the Integrative Human Microbiome Project (iHMP). A total of 546 stool samples were analyzed using a platform comprised of four complementary liquid chromatography tandem mass spectrometry (LC-MS) methods designed to measure polar metabolites and lipids. Each method used high resolution/accurate mass (HRAM) profiling to measure both metabolites of confirmed identity and yet to be identified metabolite peaks. 81,867 de-isotoped LC-MS peaks were measured, out of which 597 were annotated based on confirmation with authentic reference standards. Pooled stool extracts inserted and analyzed throughout the analysis queues to evaluate analytical reproducibility showed a median coefficient of variation of 5.1% among known metabolites and 24.2% across all 81,867 features. Owing to differences in water content and heterogeneity among stool samples, total median scaling was used to standardize the metabolomics data. In addition to being accessible at the Metabolomics Workbench repository, these metabolomics data will be incorporated into a multi’omic database (https://www.hmpdacc.org/ihmp/) that will enable the study of associations between the gut microbiome and IBD.
MuRF1-Related Metabolomic Changes in Stretched and Unloaded HL-1 Cells
STUDY_SUMMARY
Introduction: Left ventricular assist devices (LVADs) provide significant pressure and volume unloading, which reverse key structural features of heart failure, including hypertrophy, fibrosis, and altered sympathetic innervation. This has led to LVADs increasing utilization as both a bridge or destination therapy for heart failure. While distinct metabolic changes occur in the human myocardium with LVAD placement, the specific molecular mechanisms underlying these changes have not been identified. Objectives: To identify the role of MuRF1 in the metabolic changes in cardiomyocytes unloading in vitro. Methods: HL-1 atrial cardiomyocyte cells were plated on silastic membranes coated with gelatin/fibronectin and transduced with AdshRNA MuRF1 (or AdshRNA Scramble control) to knock-down MuRF1 protein to <25% of controls and subjected to 15% biaxial stretch at 1 Hz using the Flexcell FX-5000™ Compression System in serum free DMEM (or no-stretch). After 6 hours stretch, media was collected in parallel with time-matched no-stretch controls, followed by serial collections at 1, 3, 6, and 12 hours unloading (i.e. after termination of stretch). Media was analyzed by untargeted metabolomics using GC-MS. Results: After 6 hours stretch, control HL-1 cell media (AdshRNA Scramble) had 19 significantly altered metabolites compared to non-stretched control cell media (AdshRNA Scramble) by t-test, involved in: 1) glyoxylate and dicarboxylate metabolism (p=0.00087043, FDR=0.071375), 2) methane metabolism (p=0.0041113, FDR=0.089824), 3) glycine, serine and threonine metabolism (p=0.0043816, FDR=0.089824), and 4) aminoacyl-tRNA biosynthesis(p=0.0060141, FDR=0.09863). To determine the role of MuRF1 in stretch, we additionally compared the AdshRNA Scramble groups to AdshRNA MuRF1 +/- stretch at 6 hours and identified 41 significant metabolites (of 79 identified) by ANOVA, involved in: 1) phenylalanine, tyrosine, and tryptophan biosynthesis (p=0.0036482, FDR=0.05983), 2) aminoacyl-tRNA biosynthesis (p=3.74E-07, FDR=3.06E-05), and 3) valine, leucine, and isoleucine biosynthesis (p=0.0021624, FDR=0.053255). We next compared the 6 hour stretch time point of the four groups to the 1, 3, 6, and 12 hours unloading conditions to identify MuRF1-associated metabolites during the unloading period. At 12 hours of unloading (representative 1, 3, and 6 hours unloading), MuRF1 knock-down cell media had 35 (of 82 named metabolites) significantly different metabolites by ANOVA involved in 1) phenylalanine, tyrosine and tryptophan biosynthesis (p=0.0023668, FDR=0.048519), 2) aminoacyl-tRNA biosynthesis (p=0.0011403, FDR=0.0032631), 3) phenylalanine metabolism (P= 0.0011403, FDR 0.042673),and arginine and proline metabolism (p=0.0015612, FDR 0.042673). A final analysis comparing all four groups across all five time points identified 21 significant metabolites. When MuRF1 was knocked down (no stretch), these 21 metabolites were significantly increased without stretch. In response to stretch and unloading, these metabolites were further decreased in AdshRNA Scramble (control) cell media decreased. In contrast, these stretch and unloading induced decreases were attenuated in AdshRNA MuRF1 cell media. These metabolites included nine (9) amino acids (citrulline, phenylalanine, tyrosine, asparagine, 2-ketovaline, and -ketoleucine/ketoisoleucine, threonine, isoleucine, leucine), three (3) metabolic co-factors (Pantothenic acid, Myoinositol, 5,6-Dihydrouracil), and one fatty acid (stearic acid). Conclusion: These studies identify for the first time a role for MuRF1 in generating key amino acids recently reported in LVAD unloading in human myocardium using an in vitro model of atrial cardiomyocyte unloading.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister heart Institute, Department of Internal medicine
LABORATORY
Multiple Centers
LAST_NAME
Willis
FIRST_NAME
Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3915 (CwlM)
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in the M. tuberculosis genome with whole-cell lysate and assaying changes in metabolite levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might catalyze.
INSTITUTE
Weill Cornell Medical College, NY
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv0100
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in the M. tuberculosis genome with whole-cell lysate and assaying changes in metabolite levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might catalyze.
INSTITUTE
Weill Cornell Medical College, NY
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY
Metabolome profiles in urogenital schistosomiasis and associated pathologies
STUDY_SUMMARY
Metabolic fingerprint aid discovery of new biomarkers. Blood and urine were collected from volunteers in Eggua community, Nigeria, after ethical approval. LC-ESI-MS were used to analyse samples. Bioinformatics and statistical tools were used to detect important metabolites
INSTITUTE
University of Ibadan, Nigeria
DEPARTMENT
Zoology (Cell biology and Genetics unit)
LABORATORY
Centre for Materials Characterization, National Chemical Laboratory, Pune, India
LAST_NAME
Adebayo
FIRST_NAME
Adewale
ADDRESS
Cell Biology and Genetics unit, Department of zoology, University of ibadan, Nigeria/ National Centre for Cell Science, Pune, India
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv2553c
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in the M. tuberculosis genome with whole-cell lysate and assaying changes in metabolite levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might catalyze.
INSTITUTE
Weill Cornell Medical College, NY
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv2247
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in the M. tuberculosis genome with whole-cell lysate and assaying changes in metabolite levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might catalyze.
INSTITUTE
Weill Cornell Medical College, NY
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3208
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in the M. tuberculosis genome with whole-cell lysate and assaying changes in metabolite levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might catalyze.
INSTITUTE
Weill Cornell Medical College, NY
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3285
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in the M. tuberculosis genome with whole-cell lysate and assaying changes in metabolite levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might catalyze.
INSTITUTE
Weill Cornell Medical College, NY
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3651
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in the M. tuberculosis genome with whole-cell lysate and assaying changes in metabolite levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might catalyze.
INSTITUTE
Weill Cornell Medical College, NY
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3799c
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in the M. tuberculosis genome with whole-cell lysate and assaying changes in metabolite levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might catalyze.
INSTITUTE
Weill Cornell Medical College, NY
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3916c
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in the M. tuberculosis genome with whole-cell lysate and assaying changes in metabolite levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might catalyze.
INSTITUTE
Weill Cornell Medical College, NY
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY
Isolated T cells were activated for 48-72 hours in the presence and absence of 5mM DFMO, an ODC inhibitor
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LAST_NAME
Hesterberg
FIRST_NAME
Rebecca
ADDRESS
12902 Magnolia Dr
EMAIL
rebecca.hesterberg@moffitt.org
PHONE
813-270-9181
NUM_GROUPS
4
TOTAL_SUBJECTS
16
STUDY_COMMENTS
OT-1 mice express a transgenic T cell receptor in all CD8+ T cells that binds with high affinity to a peptide derived from the protein ovalbumin (SIINFEKL).
Determine metabolomics signatures important for the ability of Streptococus gallolyticus to promote colon cancer cell proliferation
STUDY_SUMMARY
HT29 cells were treated with Sg TX20005 stationary phase, Sg TX20005 exponential phase (negative control), and Sg TX20008 stationary phase (negative control), and media only (baseline control). The cells were washed and aliquoted. One aliquot was pelleted and stored at -80C for metabolomics analysis. DNA was also extracted from the other aliquot for DNA methylation studies.
Pediatric obesity has more than doubled in children and tripled in adolescents over the past 30 years. Recent findings demonstrate that differences in energy harvesting bacteria promote obesity in the host and appear to be influenced by early life factors such as mode of delivery, maternal obesity, and breastfeeding. The goal of this proposal is to investigate how human milk impacts the infant gut microbiome during the first 12-months of life and identify the microbe-host interactions that mediates the protective role of breastfeeding on infant adiposity. The results of this exploratory study will characterize factors that influence microbial transmission between mothers and offspring and identify human milk compounds that stabilize a healthy infant microbiome with potential to reduce pediatric obesity.
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LABORATORY
R1-187
LAST_NAME
Carney
FIRST_NAME
Olivia
ADDRESS
Clinical and Translational Research Building, University of Florida College of Medicine, 2004 Mowry Road, Gainesville, FL 32608
EMAIL
ocarney1@ufl.edu
PHONE
352-294-8361
NUM_GROUPS
3
TOTAL_SUBJECTS
12
STUDY_COMMENTS
12 samples (4 mothers with 3 human milk fractions: fat, skim and whole)
Lipidomics of inflammation-induced optic nerve regeneration
STUDY_TYPE
untargeted LC-MS/MS profiling
STUDY_SUMMARY
In adult mammals, retinal ganglion cells (RGCs) fail to regenerate their axons when damaged. As a result, RGCs die after acute injury and in progressive degenerative diseases such as glaucoma; such damage can lead to permanent vision loss and blindness. Little is known about the roles of lipids in axon injury and repair despite their fundamental importance in composition of cell membranes, myelin sheaths and mediation of signaling pathways. Study of the lipidome in the biology of optic nerve (ON) regeneration has been largely neglected. A better understanding of the roles that lipids play in RGC biology may enhance understanding of RGC-related diseases and point to novel treatments. Established experimental models of ON regeneration allow exploration of molecular determinants of RGC axon regenerative success and failure. In this study, we used high-resolution liquid chromatography-tandem mass spectrometry to analyze lipidomic profiles of the ON and retina in an ON crush model with and without intravitreal Zymosan injections to enhance regeneration. Our results reveal profound remodeling of retina and ON lipidomes that occur after injury. In the retina, Zymosan treatment largely abrogates widespread lipidome alterations. In the ON, Zymosan induces lipid profiles that are distinct from those observed in naïve and vehicle-injected crush controls. We have identified a number of lipid species, classes and fatty acids that may be involved in the mechanisms of axon damage and repair. Lipids upregulated during RGC regeneration may be interesting candidates for further functional studies.
U13C Glucose Tracing of Young and Old Pancreatic Islets
STUDY_SUMMARY
Pancreatic islets from young and old mice were traced with either 2.8mM or 16.8mM U13C glucose to determine the effect of age upon glucose metabolism in basal and stimulated states.
Timecourse of U13C glucose labeling of pancreatic islets in young mice
STUDY_SUMMARY
Pancreatic islets from young mice were traced with 16.8mM U13C glucose over a 90 minute timecourse to determine the rate of metabolite labeling during glucose stimulation.
Impact of thiamine metabolites and spent medium from Chlorella sorokiniana on metabolism in the green algae Auxenochlorella prototheciodes (part I)
STUDY_SUMMARY
The purpose of this study is to determine how thiamine metabolites impact central metabolism in Auxenochlorella protothecoides when grown in the presence of glucose. We hypothesize that thiamine metabolites alleviate bottlenecks in the TCA cycle and gluconeogensis, thus allowing for greater starch production when they are present. Cells were grown in bioreactors: 3 control cultures with no thiamine metabolites, 3 cultures received thiamine, 3 recieved HMP, and 3 were grown on residual medium from another algae species - Chlorella sorokiniana. We suspect that this residual medium also contains thiamine metabolites. Samples were taken daily from each of these 12 cultures over a 5 day time course so that we can observe build-up of metabolites over time.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Impact of thiamine metabolites and spent medium from Chlorella sorokiniana on metabolism in the green algae Auxenochlorella prototheciodes (part II)
STUDY_SUMMARY
The purpose of this study is to determine how thiamine metabolites impact central metabolism in Auxenochlorella protothecoides when grown in the presence of glucose. We hypothesize that thiamine metabolites alleviate bottlenecks in the TCA cycle and gluconeogensis, thus allowing for greater starch production when they are present. Cells were grown in bioreactors: 3 control cultures with no thiamine metabolites, 3 cultures received thiamine, 3 recieved HMP, and 3 were grown on residual medium from another algae species - Chlorella sorokiniana. We suspect that this residual medium also contains thiamine metabolites. Samples were taken daily from each of these 12 cultures over a 5 day time course so that we can observe build-up of metabolites over time.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
The Influence of Sugar, Artificial Sweeteners, and the Microbiome on Rodent Large Scale Profiling (part V)
STUDY_SUMMARY
Large scale profiling of rodents treated with diets rich in commonly used artifically sweeteners will be assessed in this study. We hypothesized that a specific subset of plasma metabolites are generated as a result from a diet rich in commonly used artificial sweeteners and their subsequent processing by the gut microbiome, which could ultimately lead to impaired glycemic control and negative physiological health outcomes. To test this hypothesis we administered normal, high glucose, fructose, aspartame, and acesulfame potassium diets to rats for 3 weeks, followed by a plasma collection through cardiac puncture and metabolic analysis. We also treated the gut microbiota with in rats with the same diets plus bacitracin/streptomycin to observe how alterations of the microbiome influence the plasma metabolic profile in these animals. The resulting data will give us insights into the influence of high sugar and artificial sweetener diets on homeostatic metabolic processes and dive into the symbiotic relationship of the gut microbiome with this process.
Metabolome profiles in urogenital schistosomiasis and associated pathologies (part II)
STUDY_SUMMARY
Metabolic fingerprint aid discovery of new biomarkers. Blood and urine were collected from volunteers in Eggua community, Nigeria, after ethical approval. LC-ESI-MS were used to analyse samples. Bioinformatics and statistical tools were used to detect important metabolites
INSTITUTE
University of Ibadan, Nigeria
DEPARTMENT
Zoology (Cell biology and Genetics unit)
LABORATORY
Centre for Materials Characterization, National Chemical Laboratory, Pune, India
LAST_NAME
Adebayo
FIRST_NAME
Adewale
ADDRESS
Cell Biology and Genetics unit, Department of zoology, University of ibadan, Nigeria/ National Centre for Cell Science, Pune, India
Metabolomic analysis of TB vs heathy including time to TB.
STUDY_SUMMARY
Within the GC6-74 cohorts, 4,462 HIV-negative healthy household contacts of 1,098 index TB cases were recruited from 2006 to 2012 at four African sites included in this study i.e. SUN (Stellenbosch University, South Africa), MRC (Medical Research Council Unit, The Gambia), AHRI (Armauer Hansen Research Institute, Ethiopia) and MAK (Makerere University, Uganda). The study had an exclusion period of 3 months, such that participants, who were diagnosed with active TB within 3 months of enrolment, were excluded from analysis to prevent inclusion of participants who had incipient or asymptomatic clinical TB disease at enrolment. Additional exclusion criteria were positive HIV rapid test, current or previous anti-retroviral treatment, history of TB, pregnancy, participation in drug and/or vaccine clinical trials and chronic disease diagnosis or immunosuppressive therapy within the past 6 months, and living in the study area for less than 3 months. A total of 97 individuals who developed active TB within the two year follow-up period were included in this study and matched at a ratio of 1:4 with participants who remained healthy during the 2-year follow-up period (controls); matching, by site, age class, sex, and wherever possible year of recruitment. Initial samples collected upon enrolment were termed baseline (BL) samples. Further samples were taken 6 and 18 months post-exposure, provided that the participant had remained TB free at the time of sample collection. Metabolic profiling was carried out for each study site, using either serum or plasma samples. For a small number of samples, an insufficient amount of plasma was available, so the sample was diluted using RPMI buffer.
GC6-74 metabolomics of TB vs healthy (Part 2: Serum)
STUDY_TYPE
Metabolomic analysis of TB vs healthy including time to TB.
STUDY_SUMMARY
Within the GC6-74 cohorts, 4,462 HIV-negative healthy household contacts of 1,098 index TB cases were recruited from 2006 to 2012 at four African sites included in this study i.e. SUN (Stellenbosch University, South Africa), MRC (Medical Research Council Unit, The Gambia), AHRI (Armauer Hansen Research Institute, Ethiopia) and MAK (Makerere University, Uganda). The study had an exclusion period of 3 months, such that participants, who were diagnosed with active TB within 3 months of enrolment, were excluded from analysis to prevent inclusion of participants who had incipient or asymptomatic clinical TB disease at enrolment. Additional exclusion criteria were positive HIV rapid test, current or previous anti-retroviral treatment, history of TB, pregnancy, participation in drug and/or vaccine clinical trials and chronic disease diagnosis or immunosuppressive therapy within the past 6 months, and living in the study area for less than 3 months. A total of 97 individuals who developed active TB within the two year follow-up period were included in this study and matched at a ratio of 1:4 with participants who remained healthy during the 2-year follow-up period (controls); matching, by site, age class, sex, and wherever possible year of recruitment. Initial samples collected upon enrolment were termed baseline (BL) samples. Further samples were taken 6 and 18 months post-exposure, provided that the participant had remained TB free at the time of sample collection. Metabolic profiling was carried out for each study site, using either serum or plasma samples. For a small number of samples, an insufficient amount of plasma was available, so the sample was diluted using RPMI buffer.
Metabolomic analysis of TB vs heathy including time to TB.
STUDY_SUMMARY
Within the GC6-74 cohorts, 4,462 HIV-negative healthy household contacts of 1,098 index TB cases were recruited from 2006 to 2012 at four African sites included in this study i.e. SUN (Stellenbosch University, South Africa), MRC (Medical Research Council Unit, The Gambia), AHRI (Armauer Hansen Research Institute, Ethiopia) and MAK (Makerere University, Uganda). The study had an exclusion period of 3 months, such that participants, who were diagnosed with active TB within 3 months of enrolment, were excluded from analysis to prevent inclusion of participants who had incipient or asymptomatic clinical TB disease at enrolment. Additional exclusion criteria were positive HIV rapid test, current or previous anti-retroviral treatment, history of TB, pregnancy, participation in drug and/or vaccine clinical trials and chronic disease diagnosis or immunosuppressive therapy within the past 6 months, and living in the study area for less than 3 months. A total of 97 individuals who developed active TB within the two year follow-up period were included in this study and matched at a ratio of 1:4 with participants who remained healthy during the 2-year follow-up period (controls); matching, by site, age class, sex, and wherever possible year of recruitment. Initial samples collected upon enrolment were termed baseline (BL) samples. Further samples were taken 6 and 18 months post-exposure, provided that the participant had remained TB free at the time of sample collection. Metabolic profiling was carried out for each study site, using either serum or plasma samples. For a small number of samples, an insufficient amount of plasma was available, so the sample was diluted using RPMI buffer.
Identification of unique metabolite networks between Latino and Caucasian patients with nonalcoholic fatty liver disease (NAFLD)
STUDY_TYPE
Populations comparison
STUDY_SUMMARY
Nonalcoholic fatty liver disease (NAFLD) is a spectrum of liver pathology ranging from simple steatosis to nonalcoholic steatohepatitis (NASH); the latter is characterized by inflammation and fibrosis. Risk factors for NALFD include obesity, diabetes, hyperlipidemia, and hypertension—all of which are features of metabolic syndrome. NAFLD is a very heterogeneous disease, as it presents in different patterns in males and females and in patients from different ethnicities, with unclear predictors for development and severity of disease. Previous studies have shown that NAFLD is 1.4 times more frequent in Hispanics than in Caucasians. One of the major challenges in NAFLD is the lack of accurate, noninvasive biomarkers for the detection of the most aggressive presentation, NASH. The gold standard for the diagnosis is liver biopsy, which is an invasive procedure associated with possible complications. Noninvasive diagnosis of NASH is a major unmet medical need and there are no ethnicity-specific biomarkers that can diagnose this condition and predict its progression. Therefore, the main gap in knowledge that this proposal and line of research will address is the characterizing the different plasma and liver metabolomics profile of patients with fatty liver from two ethnicities (Latinos vs. Caucasians) and of both sexes. The overall hypothesis of the present study is that the higher incidence of nonalcoholic fatty liver (NAFL) in Latino patients is reflected in a different plasma and liver metabolomics profile compared to Caucasian patients with further sex-related differences. Characterization of metabolite networks can aid in identifying the mechanistic underpinnings of sex and ethnic driven differences in NAFL which could help diagnose and establish a prognosis of this condition, especially in the critical transition from NAFL to the more aggressive nonalcoholic steatohepatitis (NASH).To address this hypothesis, plasma metabolomics profile of samples from male and female Latino and Caucasian bariatric surgery patients with NAFL and from healthy subjects will be compared. Metabolomics findings will be related with liver pathology and liver transcriptome profiles from intraoperatively obtained liver biopsies using correlation, network, and pathway analysis.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Metabolomics biomarkers and the risk of overall mortality and ESRD in CKD: results from the Progredir Cohort.
STUDY_TYPE
ongoing cohort study
STUDY_SUMMARY
454 CKD participants were originally recruited from the outpatient services from Hospital das Clinicas, Sao Paulo. Extensive baseline data and biobank were collected between 2012-2013 in the Clinical Research Center, Universitary Hospital, Sao Paulo. Participants are being actively followed for events of mortality, renal replacement therapy and CVD. Death certificates are obtained from State and National Registries. For the this uploaded data, events were determined up to May 2017 (median follow-up time of 3 y). Censoring data was considered as the last day of contact.
INSTITUTE
Sao Paulo University
DEPARTMENT
Clinical Research Center, Universitary Hospital, Sao Paulo University
LABORATORY
Laboratory of Genetics and Molecular Cardiology, Heart Institute
LAST_NAME
Titan
FIRST_NAME
Silvia
ADDRESS
255 Av Dr Eneas Carvalho Aguiar, Cerqueira César, Sao Paulo, Sp, Brazil, 05403-000
EMAIL
smotitan@gmail.com
PHONE
+1-413-362-4377
TOTAL_SUBJECTS
451
STUDY_COMMENTS
Events are overall mortality, RRT, and a composite outcome of mortality and RRT. In addition, we also provided the variable for competitive data analysis (RRT considering the competing effect of death). Please see below for description of Study Design. Cox_mortality: death events (for Cox proportional hazard models) Cox_RRT: renal replacement therapy events (for Cox proportional hazard models) Cox_composite_deathRRT: death events AND renal replacement therapy events (for Cox proportional hazard models) Competitive_RRTvs death: death or renal replacement therapy events (for competitive risk analysis) Time_death: follow-up time for death events and censored-participants (for Cox models) Time_Cox_RRT: follow-up time for renal replacement therapy events and censored-participants (for Cox models) Time_composite_deathRRT: follow-up time for death AND renal replacement therapy and censored-participants (for Cox models) Time_competitive_TRSvsDeath: follow-up time for renal replacement therapy, death or censored-participants (for competitive analysis)
Metabolomic profiles in healthy research cats receiving clindamycin with a synbiotic or a placebo: a randomized, controlled trial
STUDY_TYPE
Double-blind randomized controlled trial
STUDY_SUMMARY
Antibiotic-associated gastrointestinal signs (AAGS) occur commonly in cats. Co-administration of synbiotics is associated with decreased AAGS in people, potentially due to stabilization of the fecal microbiome and metabolome. The purpose of this double-blinded randomized-controlled trial was to compare AAGS and the fecal microbiome and metabolome between healthy cats that received clindamycin with a placebo or synbiotic. Methods. 16 healthy domestic shorthair cats from a research colony were randomized to receive 150 mg clindamycin with either a placebo (8 cats) or commercially-available synbiotic (8 cats) once daily for 21 days with reevaluation 603 days thereafter. All cats ate the same diet. Food consumption, vomiting, and fecal score were recorded. Fecal samples were collected daily on the last 3 days of baseline (days 5-7), treatment (26-28), and recovery (631-633). Sequencing of 16S rRNA genes and gas chromatography time-of-flight mass spectrometry was performed. Clinical signs, alpha and beta diversity metrics, dysbiosis indices, proportions of bacteria groups, and metabolite profiles were compared between treatment groups using repeated measures ANOVAs. Fecal metabolite pathway analysis was performed. P<0.05 was considered significant. The Benjamini & Hochberg’s False Discovery Rate was used to adjust for multiple comparisons. Results. Median age was 6 and 5 years, respectively, for cats in the placebo and synbiotic groups. Hyporexia, vomiting, diarrhea, or some combination therein were induced in all cats. Though vomiting was less in cats receiving a synbiotic, the difference was not statistically significant. Bacterial diversity decreased significantly on days 26-28 in both treatment groups. Decreases in Actinobacteria (Bifidobacterium, Collinsella, Slackia), Bacteriodetes (Bacteroides), Lachnospiraceae (Blautia, Coprococcus, Roseburia), Ruminococcaceae (Faecilobacterium, Ruminococcus), and Erysipelotrichaceae (Bulleidia, [Eubacterium]) and increases in Clostridiaceae (Clostridium) and Proteobacteria (Aeromonadales, Enterobacteriaceae) occurred in both treatment groups, with incomplete normalization by days 631-633. Derangements in short-chain fatty acid, bile acid, indole, sphingolipid, benzoic acid, cinnaminic acid, and polyamine profiles also occurred, some of which persisted through the terminal sampling timepoint and differed between treatment groups. Discussion. Cats administered clindamycin commonly develop AAGS, as well as short- and long-term dysbiosis and alterations in fecal metabolites. Despite a lack of differences in clinical signs between treatment groups, significant differences in their fecal metabolomic profiles were identified. Further investigation is warranted to determine whether antibiotic-induced dysbiosis is associated with an increased risk of future AAGS or metabolic diseases in cats and whether synbiotic administration ameliorates this risk.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
NUM_GROUPS
2
TOTAL_SUBJECTS
16 subjects/3 timepoints/47 samples
STUDY_COMMENTS
Samples from 1 subject lacking for one timepoint, resulting in a total of 47 samples. Genomic DNA was extracted from 100 mg of feces from each pooled sample using a commercially available kit (PowerSoil®, Mo Bio, Carlsbad, CA USA) according to manufacturer’s protocol for a total of 11 pooled samples.
Metabolomic Analysis of plasma samples from Non-Allergic Subjects and Profilin-Allergic Patients overexposed to Grass Pollen
STUDY_TYPE
Allergy severity comparison
STUDY_SUMMARY
Prevalence and severity of allergic diseases have increased worldwide. To date, respiratory allergy phenotypes are not fully characterized and, along with inflammation progression, treatment is increasingly complex and expensive. Profilin sensitization constitutes a good model to study the progression of allergic inflammation. Our aim was to identify the underlying mechanisms and the associated biomarkers of this progression, focusing on severe phenotypes, using transcriptomics and metabolomics. Methods: 25 subjects were included in the study. Plasma samples were analyzed using Gas and Liquid Chromatography coupled to Mass Spectrometry (GC-MS and LC-MS, respectively). Individuals were classified in 4 groups – “non-allergic”, “mild”, “moderate” and “severe” – based on their clinical history, their response to an oral challenge test with profilin, and after a refinement using a mathematical metabolomic model. PBMCs were used for microarray analysis.
INSTITUTE
The Centre of Metabolomics and Bioanalysis
DEPARTMENT
Analytical chemistry
LAST_NAME
Obeso Montero
FIRST_NAME
David
ADDRESS
Avda. Monteprincipe s/n 28668 Boadilla del Monte, Madrid, España
Metabolomic profiles in healthy research cats receiving clindamycin with a synbiotic or a placebo: a randomized, controlled trial
STUDY_TYPE
Double-blind randomized controlled trial
STUDY_SUMMARY
Antibiotic-associated gastrointestinal signs (AAGS) occur commonly in cats. Co-administration of synbiotics is associated with decreased AAGS in people, potentially due to stabilization of the fecal microbiome and metabolome. The purpose of this double-blinded randomized-controlled trial was to compare AAGS and the fecal microbiome and metabolome between healthy cats that received clindamycin with a placebo or synbiotic. Methods. 16 healthy domestic shorthair cats from a research colony were randomized to receive 150 mg clindamycin with either a placebo (8 cats) or commercially-available synbiotic (8 cats) once daily for 21 days with reevaluation 603 days thereafter. All cats ate the same diet. Food consumption, vomiting, and fecal score were recorded. Fecal samples were collected daily on the last 3 days of baseline (days 5-7), treatment (26-28), and recovery (631-633). Sequencing of 16S rRNA genes and gas chromatography time-of-flight mass spectrometry was performed. Clinical signs, alpha and beta diversity metrics, dysbiosis indices, proportions of bacteria groups, and metabolite profiles were compared between treatment groups using repeated measures ANOVAs. Fecal metabolite pathway analysis was performed. P<0.05 was considered significant. The Benjamini & Hochberg’s False Discovery Rate was used to adjust for multiple comparisons. Results. Median age was 6 and 5 years, respectively, for cats in the placebo and synbiotic groups. Hyporexia, vomiting, diarrhea, or some combination therein were induced in all cats. Though vomiting was less in cats receiving a synbiotic, the difference was not statistically significant. Bacterial diversity decreased significantly on days 26-28 in both treatment groups. Decreases in Actinobacteria (Bifidobacterium, Collinsella, Slackia), Bacteriodetes (Bacteroides), Lachnospiraceae (Blautia, Coprococcus, Roseburia), Ruminococcaceae (Faecilobacterium, Ruminococcus), and Erysipelotrichaceae (Bulleidia, [Eubacterium]) and increases in Clostridiaceae (Clostridium) and Proteobacteria (Aeromonadales, Enterobacteriaceae) occurred in both treatment groups, with incomplete normalization by days 631-633. Derangements in short-chain fatty acid, bile acid, indole, sphingolipid, benzoic acid, cinnaminic acid, and polyamine profiles also occurred, some of which persisted through the terminal sampling timepoint and differed between treatment groups. Discussion. Cats administered clindamycin commonly develop AAGS, as well as short- and long-term dysbiosis and alterations in fecal metabolites. Despite a lack of differences in clinical signs between treatment groups, significant differences in their fecal metabolomic profiles were identified. Further investigation is warranted to determine whether antibiotic-induced dysbiosis is associated with an increased risk of future AAGS or metabolic diseases in cats and whether synbiotic administration ameliorates this risk.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
NUM_GROUPS
2
TOTAL_SUBJECTS
16 subjects/3 timepoints/43 samples
STUDY_COMMENTS
Samples from 5 cats (4 placebo, 1 synbiotic) were not available at the second timepoint due to withdrawal from treatment due to severity of gastrointestinal signs. Genomic DNA was extracted from 100 mg of feces from each pooled sample using a commercially available kit (PowerSoil®, Mo Bio, Carlsbad, CA USA) according to manufacturer’s protocol for a total of 11 pooled samples.
Validating Quantitative Untargeted Lipidomics Across Nine Liquid Chromatography−High-Resolution Mass Spectrometry Platforms (Part I)
STUDY_SUMMARY
Liquid chromatography−mass spectrometry (LC−MS) methods are most often used for untargeted metabolomics and lipidomics. However, methods have not been standardized as accepted “best practice” documents, and reports lack harmonization with respect to quantitative data that enable interstudy comparisons. Researchers use a wide variety of high-resolution mass spectrometers under different operating conditions, and it is unclear if results would yield different biological conclusions depending on the instrument performance. To this end, we used 126 identical human plasma samples and 29 quality control samples from a nutritional intervention study. We investigated lipidomic data acquisitions across nine different MS instruments (1 single TOF, 1 Q/orbital ion trap, and 7 QTOF instruments). Sample preparations, chromatography conditions, and data processing methods were kept identical. Single-point internal standard calibrations were used to estimate absolute concentrations for 307 unique lipids identified by accurate mass, MS/MS spectral match, and retention times. Quantitative results were highly comparable between the LC−MS platforms tested. Using partial least-squares discriminant analysis (PLS-DA) to compare results between platforms, a 92% overlap for the most discriminating lipids based on variable importance in projection (VIP) scores was achieved for all lipids that were detected by at least two instrument platforms. Importantly, even the relative positions of individual samples on the PLS-DA projections were identical. The key for success in harmonizing results was to avoid ion saturation by carefully evaluating linear dynamic ranges using serial dilutions and adjusting the resuspension volume and/or injection volume before running actual study samples.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Validating Quantitative Untargeted Lipidomics Across Nine Liquid Chromatography−High-Resolution Mass Spectrometry Platforms (part II)
STUDY_SUMMARY
Liquid chromatography−mass spectrometry (LC−MS) methods are most often used for untargeted metabolomics and lipidomics. However, methods have not been standardized as accepted “best practice” documents, and reports lack harmonization with respect to quantitative data that enable interstudy comparisons. Researchers use a wide variety of high-resolution mass spectrometers under different operating conditions, and it is unclear if results would yield different biological conclusions depending on the instrument performance. To this end, we used 126 identical human plasma samples and 29 quality control samples from a nutritional intervention study. We investigated lipidomic data acquisitions across nine different MS instruments (1 single TOF, 1 Q/orbital ion trap, and 7 QTOF instruments). Sample preparations, chromatography conditions, and data processing methods were kept identical. Single-point internal standard calibrations were used to estimate absolute concentrations for 307 unique lipids identified by accurate mass, MS/MS spectral match, and retention times. Quantitative results were highly comparable between the LC−MS platforms tested. Using partial least-squares discriminant analysis (PLS-DA) to compare results between platforms, a 92% overlap for the most discriminating lipids based on variable importance in projection (VIP) scores was achieved for all lipids that were detected by at least two instrument platforms. Importantly, even the relative positions of individual samples on the PLS-DA projections were identical. The key for success in harmonizing results was to avoid ion saturation by carefully evaluating linear dynamic ranges using serial dilutions and adjusting the resuspension volume and/or injection volume before running actual study samples.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Validating Quantitative Untargeted Lipidomics Across Nine Liquid Chromatography−High-Resolution Mass Spectrometry Platforms (part III)
STUDY_SUMMARY
Liquid chromatography−mass spectrometry (LC−MS) methods are most often used for untargeted metabolomics and lipidomics. However, methods have not been standardized as accepted “best practice” documents, and reports lack harmonization with respect to quantitative data that enable interstudy comparisons. Researchers use a wide variety of high-resolution mass spectrometers under different operating conditions, and it is unclear if results would yield different biological conclusions depending on the instrument performance. To this end, we used 126 identical human plasma samples and 29 quality control samples from a nutritional intervention study. We investigated lipidomic data acquisitions across nine different MS instruments (1 single TOF, 1 Q/orbital ion trap, and 7 QTOF instruments). Sample preparations, chromatography conditions, and data processing methods were kept identical. Single-point internal standard calibrations were used to estimate absolute concentrations for 307 unique lipids identified by accurate mass, MS/MS spectral match, and retention times. Quantitative results were highly comparable between the LC−MS platforms tested. Using partial least-squares discriminant analysis (PLS-DA) to compare results between platforms, a 92% overlap for the most discriminating lipids based on variable importance in projection (VIP) scores was achieved for all lipids that were detected by at least two instrument platforms. Importantly, even the relative positions of individual samples on the PLS-DA projections were identical. The key for success in harmonizing results was to avoid ion saturation by carefully evaluating linear dynamic ranges using serial dilutions and adjusting the resuspension volume and/or injection volume before running actual study samples.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Validating Quantitative Untargeted Lipidomics Across Nine Liquid Chromatography−High-Resolution Mass Spectrometry Platforms (part IV)
STUDY_SUMMARY
Liquid chromatography−mass spectrometry (LC−MS) methods are most often used for untargeted metabolomics and lipidomics. However, methods have not been standardized as accepted “best practice” documents, and reports lack harmonization with respect to quantitative data that enable interstudy comparisons. Researchers use a wide variety of high-resolution mass spectrometers under different operating conditions, and it is unclear if results would yield different biological conclusions depending on the instrument performance. To this end, we used 126 identical human plasma samples and 29 quality control samples from a nutritional intervention study. We investigated lipidomic data acquisitions across nine different MS instruments (1 single TOF, 1 Q/orbital ion trap, and 7 QTOF instruments). Sample preparations, chromatography conditions, and data processing methods were kept identical. Single-point internal standard calibrations were used to estimate absolute concentrations for 307 unique lipids identified by accurate mass, MS/MS spectral match, and retention times. Quantitative results were highly comparable between the LC−MS platforms tested. Using partial least-squares discriminant analysis (PLS-DA) to compare results between platforms, a 92% overlap for the most discriminating lipids based on variable importance in projection (VIP) scores was achieved for all lipids that were detected by at least two instrument platforms. Importantly, even the relative positions of individual samples on the PLS-DA projections were identical. The key for success in harmonizing results was to avoid ion saturation by carefully evaluating linear dynamic ranges using serial dilutions and adjusting the resuspension volume and/or injection volume before running actual study samples.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Validating Quantitative Untargeted Lipidomics Across Nine Liquid Chromatography−High-Resolution Mass Spectrometry Platforms (part V)
STUDY_SUMMARY
Liquid chromatography−mass spectrometry (LC−MS) methods are most often used for untargeted metabolomics and lipidomics. However, methods have not been standardized as accepted “best practice” documents, and reports lack harmonization with respect to quantitative data that enable interstudy comparisons. Researchers use a wide variety of high-resolution mass spectrometers under different operating conditions, and it is unclear if results would yield different biological conclusions depending on the instrument performance. To this end, we used 126 identical human plasma samples and 29 quality control samples from a nutritional intervention study. We investigated lipidomic data acquisitions across nine different MS instruments (1 single TOF, 1 Q/orbital ion trap, and 7 QTOF instruments). Sample preparations, chromatography conditions, and data processing methods were kept identical. Single-point internal standard calibrations were used to estimate absolute concentrations for 307 unique lipids identified by accurate mass, MS/MS spectral match, and retention times. Quantitative results were highly comparable between the LC−MS platforms tested. Using partial least-squares discriminant analysis (PLS-DA) to compare results between platforms, a 92% overlap for the most discriminating lipids based on variable importance in projection (VIP) scores was achieved for all lipids that were detected by at least two instrument platforms. Importantly, even the relative positions of individual samples on the PLS-DA projections were identical. The key for success in harmonizing results was to avoid ion saturation by carefully evaluating linear dynamic ranges using serial dilutions and adjusting the resuspension volume and/or injection volume before running actual study samples.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Validating Quantitative Untargeted Lipidomics Across Nine Liquid Chromatography−High-Resolution Mass Spectrometry Platforms (part VI)
STUDY_SUMMARY
Liquid chromatography−mass spectrometry (LC−MS) methods are most often used for untargeted metabolomics and lipidomics. However, methods have not been standardized as accepted “best practice” documents, and reports lack harmonization with respect to quantitative data that enable interstudy comparisons. Researchers use a wide variety of high-resolution mass spectrometers under different operating conditions, and it is unclear if results would yield different biological conclusions depending on the instrument performance. To this end, we used 126 identical human plasma samples and 29 quality control samples from a nutritional intervention study. We investigated lipidomic data acquisitions across nine different MS instruments (1 single TOF, 1 Q/orbital ion trap, and 7 QTOF instruments). Sample preparations, chromatography conditions, and data processing methods were kept identical. Single-point internal standard calibrations were used to estimate absolute concentrations for 307 unique lipids identified by accurate mass, MS/MS spectral match, and retention times. Quantitative results were highly comparable between the LC−MS platforms tested. Using partial least-squares discriminant analysis (PLS-DA) to compare results between platforms, a 92% overlap for the most discriminating lipids based on variable importance in projection (VIP) scores was achieved for all lipids that were detected by at least two instrument platforms. Importantly, even the relative positions of individual samples on the PLS-DA projections were identical. The key for success in harmonizing results was to avoid ion saturation by carefully evaluating linear dynamic ranges using serial dilutions and adjusting the resuspension volume and/or injection volume before running actual study samples.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Validating Quantitative Untargeted Lipidomics Across Nine Liquid Chromatography−High-Resolution Mass Spectrometry Platforms (part VII)
STUDY_SUMMARY
Liquid chromatography−mass spectrometry (LC−MS) methods are most often used for untargeted metabolomics and lipidomics. However, methods have not been standardized as accepted “best practice” documents, and reports lack harmonization with respect to quantitative data that enable interstudy comparisons. Researchers use a wide variety of high-resolution mass spectrometers under different operating conditions, and it is unclear if results would yield different biological conclusions depending on the instrument performance. To this end, we used 126 identical human plasma samples and 29 quality control samples from a nutritional intervention study. We investigated lipidomic data acquisitions across nine different MS instruments (1 single TOF, 1 Q/orbital ion trap, and 7 QTOF instruments). Sample preparations, chromatography conditions, and data processing methods were kept identical. Single-point internal standard calibrations were used to estimate absolute concentrations for 307 unique lipids identified by accurate mass, MS/MS spectral match, and retention times. Quantitative results were highly comparable between the LC−MS platforms tested. Using partial least-squares discriminant analysis (PLS-DA) to compare results between platforms, a 92% overlap for the most discriminating lipids based on variable importance in projection (VIP) scores was achieved for all lipids that were detected by at least two instrument platforms. Importantly, even the relative positions of individual samples on the PLS-DA projections were identical. The key for success in harmonizing results was to avoid ion saturation by carefully evaluating linear dynamic ranges using serial dilutions and adjusting the resuspension volume and/or injection volume before running actual study samples.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Validating Quantitative Untargeted Lipidomics Across Nine Liquid Chromatography−High-Resolution Mass Spectrometry Platforms (part VIII)
STUDY_SUMMARY
Liquid chromatography−mass spectrometry (LC−MS) methods are most often used for untargeted metabolomics and lipidomics. However, methods have not been standardized as accepted “best practice” documents, and reports lack harmonization with respect to quantitative data that enable interstudy comparisons. Researchers use a wide variety of high-resolution mass spectrometers under different operating conditions, and it is unclear if results would yield different biological conclusions depending on the instrument performance. To this end, we used 126 identical human plasma samples and 29 quality control samples from a nutritional intervention study. We investigated lipidomic data acquisitions across nine different MS instruments (1 single TOF, 1 Q/orbital ion trap, and 7 QTOF instruments). Sample preparations, chromatography conditions, and data processing methods were kept identical. Single-point internal standard calibrations were used to estimate absolute concentrations for 307 unique lipids identified by accurate mass, MS/MS spectral match, and retention times. Quantitative results were highly comparable between the LC−MS platforms tested. Using partial least-squares discriminant analysis (PLS-DA) to compare results between platforms, a 92% overlap for the most discriminating lipids based on variable importance in projection (VIP) scores was achieved for all lipids that were detected by at least two instrument platforms. Importantly, even the relative positions of individual samples on the PLS-DA projections were identical. The key for success in harmonizing results was to avoid ion saturation by carefully evaluating linear dynamic ranges using serial dilutions and adjusting the resuspension volume and/or injection volume before running actual study samples.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Validating Quantitative Untargeted Lipidomics Across Nine Liquid Chromatography−High-Resolution Mass Spectrometry Platforms (part IX)
STUDY_SUMMARY
Liquid chromatography−mass spectrometry (LC−MS) methods are most often used for untargeted metabolomics and lipidomics. However, methods have not been standardized as accepted “best practice” documents, and reports lack harmonization with respect to quantitative data that enable interstudy comparisons. Researchers use a wide variety of high-resolution mass spectrometers under different operating conditions, and it is unclear if results would yield different biological conclusions depending on the instrument performance. To this end, we used 126 identical human plasma samples and 29 quality control samples from a nutritional intervention study. We investigated lipidomic data acquisitions across nine different MS instruments (1 single TOF, 1 Q/orbital ion trap, and 7 QTOF instruments). Sample preparations, chromatography conditions, and data processing methods were kept identical. Single-point internal standard calibrations were used to estimate absolute concentrations for 307 unique lipids identified by accurate mass, MS/MS spectral match, and retention times. Quantitative results were highly comparable between the LC−MS platforms tested. Using partial least-squares discriminant analysis (PLS-DA) to compare results between platforms, a 92% overlap for the most discriminating lipids based on variable importance in projection (VIP) scores was achieved for all lipids that were detected by at least two instrument platforms. Importantly, even the relative positions of individual samples on the PLS-DA projections were identical. The key for success in harmonizing results was to avoid ion saturation by carefully evaluating linear dynamic ranges using serial dilutions and adjusting the resuspension volume and/or injection volume before running actual study samples.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Metabolomic Markers of Dietary Patterns in the Costa Rica Study
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The study will examine associations between dietary patterns and the metabolome on a random subset (n=80) of control subjects in a population-based case-control study of myocardial infarction in Costa Rican adults. Each sample will undergo complementary LC-MS-based approaches, specifically untargeted metabolite profiling and targeted lipidomic profiling. Subsequently we will test for associations between 1) previously derived dietary patterns and plasma molecular features and 2) the top plasma correlates of dietary patterns and metabolic syndrome.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Natural genetic variation in C. elegans identified genomic loci controlling metabolite levels
STUDY_TYPE
Metabolomics in C. elegans
STUDY_SUMMARY
Metabolic homeostasis is sustained by complex biological networks that respond to nutrient availability. Genetic and environmental factors may disrupt this equilibrium leading to metabolic disorders, including obesity and type 2 diabetes. To identify the genetic factors controlling metabolism, we performed quantitative genetic analysis using a population of 199 recombinant inbred lines (RILs) in the nematode Caenorhabditis elegans. We focused on the genomic regions that control metabolite levels by measuring fatty acid (FA) and amino acid (AA) composition in the RILs using targeted metabolomics. The genetically diverse RILs showed a large variation in their FA and AA levels with a heritability ranging from 32-82%. We detected strongly co-correlated metabolite clusters and 36 significant metabolite QTL (mQTL). We focused on mQTL displaying highly significant linkage and heritability, including an mQTL for the FA C14:1 on Chromosome I, and another mQTL for the FA C18:2 on Chromosome IV. Using introgression lines (ILs) we were able to narrow down both mQTL to a 1.4 Mbp and a 3.6 Mbp region, respectively. RNAi-based screening focusing on the Chromosome I mQTL identified several candidate genes for the C14:1 mQTL, including lagr-1, Y87G2A.2, nhr-265, nhr-276, and nhr-81. Overall, this systems approach provides us with a powerful platform to study the genetic basis of C. elegans metabolism. Furthermore, it allows us to investigate interventions, such as nutrients and stresses that maintain or disturb the regulatory network controlling metabolic homeostasis, and identify gene-by-environment interactions.
INSTITUTE
Academic Medical Center of Amsterdam
LAST_NAME
Gao
FIRST_NAME
Arwen
ADDRESS
Meibergdreef 9, Amsterdam, North-Holland, 1105 AZ, Netherlands
Gut microbiome structure and metabolic activity in inflammatory bowel disease
STUDY_SUMMARY
The inflammatory bowel diseases (IBD), which include Crohn’s disease (CD) and ulcerative colitis (UC), are multifactorial, chronic conditions of the gastrointestinal tract. While IBD has been associated with dramatic changes in the gut microbiota, changes in the gut metabolome -- the molecular interface between host and microbiota -- are less-well understood. To address this gap, we performed untargeted LC-MS metabolomic and shotgun metagenomic profiling of cross-sectional stool samples from discovery (n=155) and validation (n=65) cohorts of CD, UC, and non-IBD control subjects. Metabolomic and metagenomic profiles were broadly correlated with fecal calprotectin levels (a measure of gut inflammation). Across >8,000 measured metabolite features, we identified chemicals and chemical classes that were differentially abundant (DA) in IBD, including enrichments for sphingolipids and bile acids, and depletions for triacylglycerols and tetrapyrroles. While >50% of DA metabolite features were uncharacterized, many could be assigned putative roles through metabolomic “guilt-by-association” (covariation with known metabolites). DA species and functions from the metagenomic profiles reflected adaptation to oxidative stress in the IBD gut, and were individually consistent with previous findings. Integrating these data, however, we identified 122 robust associations between DA species and well-characterized DA metabolites, indicating possible mechanistic relationships that are perturbed in IBD. Finally, we found that metabolome- and metagenome-based classifiers of IBD status were highly accurate and, like the vast majority of individual trends, generalized well to the independent validation cohort. Our findings thus provide an improved understanding of perturbations of the microbiome-metabolome interface in IBD, including identification of many potential diagnostic and therapeutic targets.
Multi-Platform Physiologic and Metabolic Phenotyping Reveals Microbial Toxicity (part II)
STUDY_SUMMARY
The gut microbiota are susceptible to modulation by environmental stimuli and therefore can serve as biological sensors. Recent evidence suggests that xenobiotics can disrupt the interaction between the microbiota and host. Here, we describe an approach that combines in vitro microbial incubation (isolated cecal contents from mice), flow cytometry, and mass spectrometry- and 1H NMR-based metabolomics to evaluate xenobiotic-induced microbial toxicity. Tempol, a stabilized free radical scavenger known to remodel the microbial community structure and function in vivo, was studied to assess its direct effects on the gut microbiota. Microbiota were isolated from mouse cecum and were exposed to tempol for 4 h under strict anaerobic condition. The flow cytometry data suggested short term exposure of the microbiota to tempol is associated with disrupted membrane physiology as well as compromised metabolic activity. Mass spectrometry and NMR metabolomics revealed that tempol exposure significantly disrupted microbial metabolic activity, specifically indicated by changes in short chain fatty acids, branched chain amino acids, amino acids, nucleotides, glucose, and oligosaccharides. In addition, a mouse study with tempol (5 days gavage) showed similar microbial physiologic and metabolic changes, indicating the in vitro approach reflected in vivo conditions. Our results, through evaluation of microbial viability, physiology and metabolism, and comparison of in vitro and in vivo exposures with tempol, suggests that physiologic and metabolic phenotyping provides unique insight into gut microbiota toxicity.
INSTITUTE
The Pennsylvania State University (Penn State)
LAST_NAME
Nichols
FIRST_NAME
Robert
ADDRESS
650 toftrees ave Apt #108, State College, Pa 16802
Large Scale Profling in Muscle Tissue for Muscle Wasting in Cancer Cachexia (part-XI)
STUDY_SUMMARY
Large Scale Profiling of muscle wasting in Cancer Cachexia. Muscle samples from 10 control patients, 10 weight stable pancreatic cancer patients, and 10 pancreatic cancer patients with significant weight loss. Samples are divided evenly between males and females.
INSTITUTE
Mayo Clinic
LAST_NAME
Guttridge
FIRST_NAME
Denis
ADDRESS
520 Biomedical Research Tower 460 W. 12th Avenue Columbus, OH 43210
Large Scale Profiling in Serum for Muscle Wasting in Cancer Cachexia (part-XII)
STUDY_SUMMARY
Large Scale Profiling of muscle wasting in Cancer Cachexia. Serum samples from 10 control patients, 10 weight stable pancreatic cancer patients, and 10 pancreatic cancer patients with significant weight loss. Samples are divided evenly between males and females.
INSTITUTE
Mayo Clinic
LAST_NAME
Guttridge
FIRST_NAME
Denis
ADDRESS
520 Biomedical Research Tower 460 W. 12th Avenue Columbus, OH 43210
Lipidomic profiling of heart and plasma of mice following swim training versus pressure overload
STUDY_SUMMARY
Lipid profiling was performed on hearts and plasma from mice subjected to a physiological stimulus (4 weeks of swim exercise training) or pathological stimulus (4 weeks of pressure overload – transverse aortic constriction; TAC)
Characterization of metabolomics profile changes during development of post-traumatic epilepsy in Rat Plasma (part-I)
STUDY_SUMMARY
Characterize the metabolomics profile changes during progression of the transition from traumatic brain injury (TBI) to post-traumatic epilepsy (PTE). To do so, three experiments will be performed. PTE animal model will be developed using ferrous chloride injections. Metabolomics profile changes will be obtained before TBI, after TBI, and after PTE development These temporal changes in metabolomics profile during the course of PTE development will be collected. We will also collect cerebrospinal fluid (CSF) at each time point. In addition, we will collect the brain tissue from the center of injury, around the injury, and from the non-injured area for mass spectrometry. In this study, the rat plasma at each time point is analyzed.
Characterization of metabolomics profile changes during development of post-traumatic epilepsy in Rat Cerebrospinal Fluid (part-II)
STUDY_SUMMARY
Characterize the metabolomics profile changes during progression of the transition from traumatic brain injury (TBI) to post-traumatic epilepsy (PTE). To do so, three experiments will be performed. PTE animal model will be developed using ferrous chloride injections. Metabolomics profile changes will be obtained before TBI, after TBI, and after PTE development These temporal changes in metabolomics profile during the course of PTE development will be collected. We will also collect cerebrospinal fluid (CSF) at each time point. In addition, we will collect the brain tissue from the center of injury, around the injury, and from the non-injured area for mass spectrometry. In this study, Rat CSF is analyzed at end of study.
Characterization of metabolomics profile changes during development of post-traumatic epilepsy in Rat Brain Tissue (part-III)
STUDY_SUMMARY
Characterize the metabolomics profile changes during progression of the transition from traumatic brain injury (TBI) to post-traumatic epilepsy (PTE). To do so, three experiments will be performed. PTE animal model will be developed using ferrous chloride injections. Metabolomics profile changes will be obtained before TBI, after TBI, and after PTE development These temporal changes in metabolomics profile during the course of PTE development will be collected. We will also collect cerebrospinal fluid (CSF) at each time point. In addition, we will collect the brain tissue from the center of injury, around the injury, and from the non-injured area for mass spectrometry. In this study, the rat brain tissue at end of study is analyzed.
Influence of Data-Processing Strategies on Normalized Lipid Levels using an Open-Source LC-HRMS/MS Lipidomics Workflow
STUDY_SUMMARY
Lipidomics is an emerging field with significant potential for improving clinical diagnosis and our understanding of health and disease. While the diverse biological roles of lipids contribute to their clinical utility, the unavailability of lipid internal standards representing each species, make lipid quantitation analytically challenging. The common approach is to employ one or more internal standards for each lipid class examined and use a single point calibration for normalization (relative quantitation). To aid in standardizing and automating this relative quantitation process, we developed LipidMatch Normalizer (LMN) http://secim.ufl.edu/secim-tools/ which can be used in most open source lipidomics workflows. While the effect of lipid structure on relative quantitation has been investigated, applying LMN we show that data-processing can significantly affect lipid semi-quantitative amounts. Polarity and adduct choice had the greatest effect on normalized levels; when calculated using positive versus negative ion mode data, one fourth of lipids had greater than 50 % difference in normalized levels. Based on our study, sodium adducts should not be used for statistics when sodium is not added intentionally to the system, as lipid levels calculated using sodium adducts did not correlate with lipid levels calculated using any other adduct. Relative quantification using smoothing versus not smoothing, and peak area versus peak height, showed minimal differences, except when using peak area for overlapping isomers which were difficult to deconvolute. By characterizing sources or variation introduced during data-processing and introducing automated tools, this work helps increase through-put and improve data-quality for determining relative changes across groups.
INSTITUTE
University of Florida
DEPARTMENT
Chemistry
LABORATORY
Richard Yost Laboratory
LAST_NAME
Levy
FIRST_NAME
Allison
ADDRESS
214 Leigh Hall, PO Box 117200, Gainesville, Florida, 32611, USA
An integrated, high-throughput strategy for multi-omic systems level analysis
STUDY_SUMMARY
This report details the automation, benchmarking, and application of a strategy for transcriptomic, proteomic, and metabolomic analyses from a common sample. The approach, Sample Preparation for multi-Omics Technologies (SPOT), provides equivalent performance to typical individual omic preparation methods, but it greatly enhances throughput and minimizes the resources required for multi-omic experiments. SPOT was applied to a multi-omics time course experiment for zinc-treated HL60 cells.
Untargeted Discovery in Primary Metabolism: Collision Cross Section as a Molecular Descriptor in Ion Mobility Spectrometry
STUDY_TYPE
Database Library
STUDY_SUMMARY
In this work we have established a collision cross section (CCS) library of primary metabolites based on analytical standards in the Mass Spectrometry Metabolite Library of Standards (MSMLS). Using a commercially available ion mobility-mass spectrometer (IM-MS, Agilent 6560), from the 554 unique compounds in the MSMLS plate library we obtained a total of 1246 CCS measurements over a wide range of biochemical classes and adduct types. Resulting data analysis showed that the curated CCS library provides broad molecular coverage of metabolic pathways and highlights intrinsic mass/mobility relationships for specific metabolite superclasses. The separation and characterization of isomeric metabolites were assessed as well as an investigation to determine the analytical separation efficiency in both the mass (m/z) and mobility (CCS/ΔCCS) dimension required for untargeted metabolomic analyses. To further demonstrate the analytical utility of CCS as an additional molecular descriptor, a well characterized biological sample of human plasma serum (NIST 1950) was examined by LC-IM-MS and a detailed analysis of carbohydrate isomers by ion mobility is presented.
INSTITUTE
Vanderbilt University
DEPARTMENT
Chemistry
LABORATORY
McLean Laboratory
LAST_NAME
Dodds
FIRST_NAME
James
ADDRESS
7330 Stevenson Ct., Nashville, Tennessee, 37235, USA
Metabolome analysis on multi-connected biparental chromosome segment substitution line populations in rice
STUDY_SUMMARY
rice flag leaves at heading stage from three chromosome substitution line populations, which were respectively constructed by introducing genomic segments from japonica cultivar Niponbare, indica cultivar Minghui 63 and wild accession ACC10, to an indica cultivar Zhenshan 97, were collected. Metabolomics profile was conducted to generate quantitative trait loci that may affect contents of metabolites, and candidate genes were assigned.
Determination of mode of action of anti-malalrial drugs using untargeted metabolomics
STUDY_SUMMARY
The mode of action of a representative active compound was investigated using an unbiased metabolomics approach, which has previously been shown to reveal both novel and established modes of action of antimalarials (Creek et al 2016, DOI: 10.1128/AAC.01226-16). The active antimalarial OSM-S-313, and the inactive analogue OSM-S-291, were incubated with trophozoite stage P. falciparum parasites for five hours alongside reference compounds including atovaquone (ATV), chloroquine (CQ), dihydroartemisisin (DHA) and three PfATP4 inhibitors, MMV00073, MMV397264 and MMV390482. Metabolomics analysis of cell pellets and spent media allowed reproducible detection of diverse metabolites from a range of metabolic pathways, with the most significant OSM-S-313-induced perturbations observed within peptide, lipid and energy metabolism, suggesting a specific impact on parasite metabolism.
INSTITUTE
Monash University
LAST_NAME
Creek
FIRST_NAME
Darren
ADDRESS
Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Melbourne, Victoria, 3052, Australia
PAMP-triggered changes in the exometabolome of Arabidopsis suspension cells
STUDY_SUMMARY
The goal of this study was to determine how the exometabolome of defense-elicited Arabidopsis suspension cells inhibits virulence gene expression and growth of a plant pathogenic bacterium Pseudomonas syringae. Arabidopsis T87 suspension cells were treated with the pathogen-associated molecular pattern elf26 or a DMSO-control treatment for six hours, then incubated in fresh media for one hour. The conditioned medium (exudate) was collected from each culture by centrifugation and 0.22 um filter to remove plant cells. These samples are designated T=6 mock and T=6 elf26 in our experimental design. We also prepared samples in the same manner from control-treated cells except without any pre-treatment time prior to one hour exudate production. These samples are labeled T=0 mock. A total of seven biological replicates of each treatment condition were analyzed, with each replicate prepared from cells grown in separate flasks. The exudates were prepared in four independent experiments performed on separate days (1 biological replicate from first experiment, 2 biological replicates from each of the 3 remaining experiments). Four samples of the culture medium, one from each of the four independent experiments, are included.
Development of a weaned pig model of enterotoxigenic E.coli-induced environmental enteropathy
STUDY_TYPE
Animal Model
STUDY_SUMMARY
Environmental Enteropathy (EE) is a subclinical condition primarily effecting developing countries believed to be caused by chronic fecal-oral contamination. The condition is characterized by chronic gut inflammation, malabsorption, stunting of growth, stunted villi, and reduced efficacy of oral vaccines. Due to the similarity of the gastrointestinal tract and immune response of swine and humans, the piglet is an attractive model for studying this condition. In this present study, piglets were challenged with either a chronic or acute dose of pathogenic E.coli in an attempt to mimic the symptoms of EE over a 7 day trial period. Throughout the study a number of biological samples were collected for analysis and are presented here, including feces for untargeted metabolomics analysis.
Two groups of rats were fed either a high salt diet or a low salt diet. This study aims to look at salt intake in correlation to altering other metabolites and the onset of hypertension
Metabolite Extractions data from the Strains Synechococcus sp. PCC 7002, Synechococcus elongatus PCC 11801 (New strain, Manuscript submitted) and Synechococcus elongatus PCC 7942
Lipidomics for wildlife disease etiology and biomarker discovery: a case study of pansteatitis outbreak in South Africa (part-II)
STUDY_TYPE
lipidomics
STUDY_SUMMARY
Lipidomics is a promising tool to determine biomarkers and elucidate mechanisms associated with anthropogenic-induced stress in wildlife. Therefore, we examine the application of lipidomics for in situ studies on Mozambique tilapia (Oreochromis mossambicus) in Loskop Dam, South Africa. Mortality events of aquatic life associated with an environmentally-derived inflammatory disease, pansteatitis, have occurred in this area. The lipidome of adipose tissue (n = 31) and plasma (n = 51) from tilapia collected from at Loskop Dam were characterized using state of the art liquid chromatography coupled to high-resolution tandem mass spectrometry. Lipid profiles reflected pansteatitis severity and were significantly different between diseased and healthy individuals. Over 13 classes of lipids associated with inflammation, cell death, and/or oxidative damage were upregulated in pansteatitis-affected adipose tissue, including ether-lipids, short-chained triglyceride oxidation products, sphingolipids, and acylcarnitines. Ceramides showed a 1000-fold increase in the most affected adipose tissues, illustrating its potential as sensitive and novel indicators of disease severity. In plasma, triglycerides were found to be downregulated in pansteatitis-affected tilapia. As comprehensive coverage of the lipidome aids in the elucidation of possible disease mechanisms, application of lipidomics could be applied to the understanding of other environmentally-derived inflammatory conditions, such as those caused by obesogens.
INSTITUTE
South East Center for Integrated Metabolomics
DEPARTMENT
Department of Pathology, Immunology and Laboratory Medicine
LABORATORY
SECIM
LAST_NAME
Koelmel
FIRST_NAME
Jeremy
ADDRESS
Department of Pathology, Immunology and Laboratory Medicine, University of Florida, 1395 Center Dr, Room M641c
The proteomic and metabolomic characterization of exercise-induced sweat (part -I)
STUDY_SUMMARY
Proteomic and Metabolomic analysis of exercise-induced sweat to evaluate analyte correlation with human performance parameters. Sweat was collected from participants on a treadmill at low, medium, and hard speed and incline. Sweat was analyzed by untagged HILIC LC-MS.
INSTITUTE
UES Inc, Air Force Research Laboratory
LAST_NAME
Harshman
FIRST_NAME
Sean
ADDRESS
2510 Fifth Street, Area B, Building 840, WPAFB, OH 45433
Treatment comparison of Guinea grass planted at University of Sao Paulo Brazil 4 Ambient temp and CO2 plots, 4 elevated CO2 (600 ppm) plots, 4 elevated Temp plots (+2C),4 elevated CO2 and Temp plots. Untargeted metabolomics(GC-MS),de novo transcriptomics, and RNAseq taken at 30(A)(2014-05-22) and 50(B)(2014-07-14)days post treatment exposure. Dried leaf material sent to Uni Illinois-UC. GC-MS protocol followed as stated in Ulanov et al. (2010) J of Plant Phys.
INSTITUTE
University of Illinois at Urbana-Champaign (UIUC)
DEPARTMENT
Plant Biology
LABORATORY
Ainsworth USDA ARS Global Change and Photosynthesis Research Unit
Lipid profiling of Wnt3a-induced optic nerve regeneration
STUDY_TYPE
untargeted lipid profiling
STUDY_SUMMARY
We analyzed lipid profiles of mouse retina and optic nerve for 2 time points - 7 and 15 days post-crush, and 3 conditions - intact control, optic nerve crush + vehicle (saline) intravitreal injection, optic nerve crush + 20 ng of Wnt3a injection.
INSTITUTE
University of Miami
DEPARTMENT
Ophthalmology, Bascom Palmer Eye Institute
LABORATORY
Sanjoy K. Bhattacharya lab
LAST_NAME
Bhattacharya
FIRST_NAME
Sanjoy
ADDRESS
Bascom Palmer Eye Institute (McKnight Bldg.), 1638 NW 10th Avenue, Suite 707A, University of Miami, Miami, FL, 33136
Integrated metabolome and transcriptome analyses provide novel insight into colon cancer modulation by the gut microbiota
STUDY_SUMMARY
Colon cancer onset and progression is strongly associated with the presence, absence, or relative abundances of certain microbial taxa in the gastrointestinal tract. However, specific mechanisms affecting disease susceptibility related to complex commensal bacterial mixtures are poorly understood. We used a multi-omics approach to determine how differences in the complex gut microbiome (GM) influence the metabolome and host transcriptome and ultimately affect susceptibility to adenoma development. Fecal samples collected from a preclinical rat model of colon cancer harboring distinct complex GMs were analyzed using ultra-high performance liquid chromatography mass spectrometry (UHPLC-MS). We collected samples prior to observable disease onset and identified putative metabolite profiles that predicted future disease severity, independent of GM status. Transcriptome analyses performed after disease onset from normal epithelium and tumor tissues between the high and low tumor GMs suggests that the GM is also correlated with altered host gene expression. Integrated pathway (IP) analyses of the metabolome and transcriptome based on putatively identified metabolic features indicate that bile acid biosynthesis was enriched in rats with high tumors (GM:F344) along with increased fatty acid metabolism and mucin biosynthesis. These data emphasize the utility of using untargeted metabolomics to reveal signatures of susceptibility and resistance and integrated analysis reveals common pathways that are likely to be universal targets for intervention.
Dynamic labeling of intracellular metabolites in PCC 7002
STUDY_TYPE
Timecourse experiment
STUDY_SUMMARY
The experiment was conducted in a reactor at a metabolic steady state (OD 730 nm = 0.8). 13C labeled sodium bicarbonate was used as a tracer. Tracer concentration was 1 g/L. After the introduction of the tracer, the samples were collected at time point : 0, 60, 120, 180 and 240 secs. Samples were quenched with methanol and extracted using methanol-chloroform-water method. Extracts were stored at -80 degree C till LCMS analysis.
Combined NMR and MS Analysis of PC patien serum (part-II)
STUDY_SUMMARY
Serum of two groups of patients were analyzed using MS and NMR to find predictive markers of recurrence. Factor Sample Type in study design section refers to samples with Recurrence (R)/ No Recurrence (NR)/ Blank (B) / Pooled (P).
In this study, SETD2 null isogenic 38E/38F clones derived from 786-O cells were generated by zinc finger nucleases, and the cellular metabolic changes of 786-O (WT) and 38E/38F isogenic cell lines (n=3 per group) were analyzed by GC-MS-based targeted metabolomics.
Metabolomics and 16S rRNA sequencing of human colorectal cancers and adjacent mucosa
STUDY_SUMMARY
Colorectal cancer (CRC) is ranked the third most common cancer in human worldwide. However, the exact mechanisms of CRC are not well established. Furthermore, there may be differences between mechanisms of CRC in the Asian and in the Western populations. In the present study, we utilized a liquid chromatography-mass spectrometry (LC-MS) metabolomic approach supported by the 16S rRNA next-generation sequencing to investigate the functional and taxonomical differences between paired tumor and unaffected (normal) surgical biopsy tissues from 17 Malaysian patients. Metabolomic differences associated with steroid biosynthesis, terpenoid biosynthesis and bile metabolism could be attributed to microbiome differences between normal and tumor sites. The relative abundances of Anaerotruncus, Intestinimonas and Oscillibacter displayed significant relationships with both steroid biosynthesis and terpenoid and triterpenoid biosynthesis pathways. Metabolites involved in serotonergic synapse/ tryptophan metabolism (Serotonin and 5-Hydroxy-3-indoleacetic acid [5-HIAA]) were only detected in normal tissue samples. On the other hand, S-Adenosyl-L-homocysteine (SAH), a metabolite involves in methionine metabolism and methylation, was frequently increased in tumor relative to normal tissues. In conclusion, this study suggests that local microbiome dysbiosis may contribute to functional changes at the cancer sites. Results from the current study also contributed to the list of metabolites that are found to differ between normal and tumor sites in CRC and supported our quest for understanding the mechanisms of carcinogenesis.
INSTITUTE
University of Malaya
LAST_NAME
Loke
FIRST_NAME
Mun Fai
ADDRESS
Department of Medical Microbiology, Faculty of Medicine, Kuala Lumpur, Federal Territory, 50603, Malaysia
Host NLRP6 exacerbates graft-versus-host disease independent of microbial diversity
STUDY_SUMMARY
Host NLRP6 regulates innate immune responses and gastrointestinal (GI) homeostasis. It plays a protective role in pathogenic processes such as intestinal colitis and tumorigenesis in a microbiome dependent manner. Host innate immunity and changes in microbial diversity also play a role in the severity of allo-immune-mediated gastrointestinal pathogenic process, namely graft-versus-host disease (GVHD), the principal toxicity after allogeneic bone marrow transplantation (allo-BMT). Herein, we examined the role of NLRP6 in multiple murine models of allo-BMT. In contrast to its role in intestinal colitis, host NLRP6 aggravated GI GVHD. NLRP6-deficient animals showed improved intestinal barrier function, increased levels of tissue repair associated proteins and preserved Goblet and Paneth cell numbers in the GI tract after allo-BMT. The impact of host NLRP6 deficiency in mitigating GVHD was observed regardless of co-housing, antibiotic treatment, or colonizing littermate germ free wild type (WT) and NLRP6 deficient hosts with fecal microbial transplantation from SPF WT and Nlrp6-/- animals. Chimera studies were performed to assess the role of NLRP6 expression on host hematopoietic and non-hematopoietic cells. The allogeneic [B6Ly5.2→Nlrp6-/-] animals demonstrated significantly improved survival compared to the allogeneic [B6Ly5.2→B6] animals, demonstrating that the absence of NLRP6 in host non-hematopoietic cells is crucial for the protection against GVHD, but did not alter the therapeutic graft-versus-tumor effects after BMT. Our results unveil a novel role for NLRP6 and demonstrate a pathogenic role in GVHD that is independent of variations in its intestinal microbiome in contrast to its well-appreciated microbiome-dependent protective role in intestinal colitis and tumorigenesis.
Impact of genetic suppression (shRNA) of ALDH1A1 expression in human colon cancer cell line (COLO320)
STUDY_TYPE
Untargeted metabolomics
STUDY_SUMMARY
Using a multi-omics approach, we have investigated the impact of genetic suppression (shRNA) of ALDH1A1 expression on transcriptomics, proteomics and untargeted metabolomics analyses in a human colon cancer cell line (COLO320). The present study (i) generates an integrative omic profile of scramble shRNA vs. ALDH1A1 shRNA COLO320 cells, and (ii) identifies possible alterations in biological pathways caused by suppression of ALDH1A1 expression.
Early Mechanistic Events Induced by Secondhand Smoke Prevalent Low Molecular Weight Polycyclic Aromatic Hydrocarbons in Mouse Lung Epithelial Cells (part-I)
STUDY_SUMMARY
We evaluated lung epithelial cells exposed to low molecular weight polycyclic aromatic hydrocarbons and what lipid metabolites were produced following early exposure, prior to metabolism. We used 40 uM 1-methylanthracene and fluoranthene (1:1 ratio)for 30 min, 1h, and 4 h time points for the global untargeted metabolomics study (AKB study 1).
Data resource for fully 13C labelled and non-labelled plant tissues (part-I)
STUDY_SUMMARY
LC-MS/MS data files of fully 13C labelled and 12C plant tissues, which were utilized to determine the carbon element number for metabolite characterizations.
Metabolomics of Metabolic Risk in Patients Taking Atypical Antipsychotics (part II)
STUDY_SUMMARY
STUDY OBJECTIVE Patients with schizophrenia are known to have higher rates of metabolic disease than the general population. Contributing factors likely include lifestyle and atypical antipsychotic (AAP) use, but the underlying mechanisms are unknown. The objective of this study was to identify metabolomics variability in adult patients with schizophrenia who were taking AAPs and grouped by fasting insulin concentration, our surrogate marker for metabolic risk. DESIGN Metabolomics analysis. PARTICIPANTS Ninety-four adult patients with schizophrenia who were taking an AAP for at least 6 months, with no changes in their antipsychotic regimen for the previous 8 weeks, and who did not require treatment with insulin. Twenty age- and sex-matched nonobese (10 subjects) and obese (10 subjects) controls without cardiovascular disease or mental health diagnoses were used to match the body mass index range of the patients with schizophrenia to account for metabolite concentration differences attributable to body mass index. MEASUREMENTS AND MAIN RESULTS Existing serum samples were used to identify aqueous metabolites (to differentiate fasting insulin concentration quartiles) and fatty acids with quantitative nuclear magnetic resonance (NMR) and gas chromatography (GC) methods, respectively. To exclude metabolites from our pathway mapping analysis that were due to variability in weight, we also subjected serum samples from the nonobese and obese controls to the same analyses. Patients with schizophrenia had a median age of 47.0 (interquartile range 41.0-52.0) years. Using a false discovery rate threshold of <25%, 10 metabolites, not attributable to weight, differentiated insulin concentration quartiles in patients with schizophrenia and identified variability in one-carbon metabolism between groups. Patients with higher fasting insulin concentrations (quartiles 3 and 4) also trended toward having higher levels of saturated fatty acids compared with patients with lower fasting insulin concentrations (quartiles 1 and 2). CONCLUSION These results illustrate the utility of metabolomics to identify pathways underlying variable fasting insulin concentration in patients with schizophrenia. Importantly, no significant difference in AAP exposure was observed among groups, suggesting that current antipsychotic use may not be a primary factor that differentiates middle-aged adult patients with schizophrenia by fasting insulin concentration. This article is protected by copyright. All rights reserved. As published in Pharmacotherapy. 2018 Jun;38(6):638-650.
Untargeted LC-MS to compare blood collection tube and processing time – HILIC & C18
STUDY_SUMMARY
Blood was collected from three healthy volunteers in 3 blood collection tubes: serum separator tube SST (serum), EDTA (plasma), and P100 (plasma) and stored at 4 degrees for 0, 0.5, 1, 2, 4, and 24 hours prior to centrifugation. Compounds were extracted using liquid-liquid extraction to obtain a hydrophilic and a hydrophobic fraction and analyzed using liquid chromatography mass spectrometry. Differences among the blood collection tubes and sample processing time were evaluated (ANOVA with Bonferroni FWER ≤ 0.05 and ANOVA with Benjamini Hochberg FDR ≤ 0.1, respectively).
Identification of potential sepsis biomarkers in burn injury conditions.
STUDY_SUMMARY
12 mice were subjected to one of four treatment groups: no burn injury:no injection, burn injury:no infection, no burn injury:infection, and burn injury:infection. The researchers in this study are looking for metabolites in serum that could indicate sepsis in mice with burn injuries.
Physiological and metabolic response of crab megalopae and juveniles to ocean acidification
STUDY_SUMMARY
Young crab samples were placed into 1 of 4 treatment groups to understand their metabolic response to ocean acidification and dissolved oxygen content.
An untargeted metabolomics approach was utilized to determine urinary metabolites that could serve as small molecule biomarkers for treatment response to standard tuberculosis treatment. However, the majority of metabolites that most accurately distinguished patient samples at time of diagnosis from those at one month after the start of therapy lacked structural identification. The detection of unknown metabolite structures is a well-known limitation of untargeted metabolomics, and underscores a need for continued elucidation of novel metabolite structures. In this study, we sought to define the structure of a urine metabolite with an experimentally determined mass of 202.1326 Da, classified as molecular feature (MF) 874.3547. Using mass spectrometry combined with enzymatic digestions, the metabolite was structurally characterized as a seryl-leucine core 1 O-glycosylated peptide (SLC1G) of human origin.
The aim of this project was to characterize lipid profiles of the retinal ganglion cells (RGCs) with different regenerative capacity. RGCs were FACS-sorted (7,000 cells/sample) from mice of OPN4 Cre tdT and Thy1-CFP genotype. The treatment conditions included intact, optic nerve crush (ONC) and ONC plus CNTF to promote regeneration. Samples were then subject to lipid extraction and analyzed using LC-MS/MS, followed by identification and relative quantification in LipidSearch software.
Investigating link between metabolism and circadian rhythm in Drosophila melanogaster
STUDY_SUMMARY
We are investigating the link between metabolism, circadian rhythm, and a high-fat diet with an emphasis on the role of metabolites that affect protein post translational modifications. We've hypothesized that protein modifications, which are critical to circadian clock functions, can be affected by different metabolic profiles, such as an excess or lack of fat in the diet, that ultimately regulate changes in circadian biology.
INSTITUTE
University of California, Davis
DEPARTMENT
College of Biological Sciences
LAST_NAME
Contreras
FIRST_NAME
Adam
ADDRESS
202 Life Sciences Building, Kleiber Hall Drive, Davis, CA, 95616
The nutrition value of fish fillet is related to fish maturation or fish age? Integrated analysis of transcriptomics and metabolomics in blunt snout bream (Megalobrama amblycephala)
STUDY_SUMMARY
With the improvement of living standards, people’s demand for food nutrient is getting higher and higher. Fish is one kind of protein-rich food and is increasingly favored by consumers. It has been well recognized that flesh composition of fish is closely related to its maturation and growth stages, but few researches have explored these differences. Besides, hormone residues in fish after artificial inducing reproduction also attract consumers’ concern. In this study, we try to address these concerns by using a combination of transcriptomics and metabolomics analysis to identify the key pathways, genes, and metabolites regulation which may affect flesh nutrition of one typical aquaculture species in China, blunt snout bream (Megalobrama amblycephala).
INSTITUTE
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education
LAST_NAME
guan
FIRST_NAME
ningnan
ADDRESS
College of Fisheries,Huazhong Agricultural University 1 Shizishan Road Hongshan District Wuhan, Hubei
Metabolomics profile of umbilical cord blood is associated with maternal pre-pregnant obesity in a perspective multi-ethnic cohort displaying health disparities
STUDY_SUMMARY
Maternal obesity has become a growing global health concern that impacts fetal health and subsequently predisposes the offspring to medical conditions later in life. However, the molecular link between abnormal fetal metabolomic profiles and maternal obesity has not yet been fully elucidated. In this study, we report new discoveries from the newborn cord blood metabolomes associated with a case-control maternal obesity cohort, collected from multi-ethnic populations in Hawaii, including rarely reported Native Hawaiian and other Pacific Islanders (NHPI). This cohort displays significant maternal obesity disparities by subjects’ residential area average income and health insurance. An elastic net penalized logistic regression model was constructed to associate cord blood metabolomics and demographic/physiological information to maternal obesity, with accuracy as high as 0.947. We identify 29 metabolites as early-life biomarkers manifesting intrauterine effect of maternal obesity.
Growth cone-enriched lipidome of embryonic to early postnatal mouse brain
STUDY_SUMMARY
A growth cone (GC) is a part of a neuron considered a hub for axon growth, motility and guidance functions. Unraveling the molecular composition of GCs and events through which active GCs transition to terminal synapses is of importance to developmental and regenerative neuroscience research. Here, we present a dataset on the lipid profiling of the growth cone-enriched fractions derived from E18, P0, P3, P6 and P9 C57BL/6J mouse brains. For comparison, we analyzed non-growth cone membranes.
Metabolomics profiles of patients with Wilson disease reveal a distinct metabolic signature
STUDY_SUMMARY
This study is comparing the plasma metabolomics profile of patients with the genetic disorder, Wilson disease, compared to healthy subjects matched by age, sex, and BMI. Wilson disease is caused by a defect in a copper transporter leading to copper accumulation in the liver and brain leading to liver and/or neuropsychiatric symptoms. Mitochondrial defects are well-documented in Wilson disease. We hypothesize the acylcarnitine and primary metabolite profile will differ between patients with Wilson disease and healthy subjects and that these differences may indicate specific metabolic abnormalities.
Reprogrammed Lipid Metabolism in Bladder Cancer with Cisplatin Resistance
STUDY_SUMMARY
This study conducted comprehensive and comparative lipidomic profiling of two isogenic human T24 bladder cell lines, which are characterized as sensitive or resistant to the cisplatin-induced cell apoptosis.
INSTITUTE
Cedars-Sinai Medical Center
DEPARTMENT
Departments of Surgery and Biomedical Sciences
LAST_NAME
Kim
FIRST_NAME
Jayoung
ADDRESS
8700 Beverly Blvd., Davis 5071 Los Angeles, CA 90048, USA
Identification of urine metabolites in patients with interstitial cystitis using untargeted metabolomics (part I)
STUDY_SUMMARY
Urine metabolites are used in many clinical and biomedical studies, but usually only for a few classic compounds. Metabolomics detects vastly more metabolic signals that may be used to precisely define the health status of individuals. However, many compounds remain unidentified, hampering biochemical conclusions. Here, we annotate all metabolites detected using an untargeted metabolomics approach with a charged surface hybrid (CSH) assay on a Q Exactive HF mass spectrometry.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Blaženović
FIRST_NAME
Ivana
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Identification of urine metabolites in patients with interstitial cystitis using untargeted metabolomics (part II)
STUDY_SUMMARY
Urine metabolites are used in many clinical and biomedical studies, but usually only for a few classic compounds. Metabolomics detects vastly more metabolic signals that may be used to precisely define the health status of individuals. However, many compounds remain unidentified, hampering biochemical conclusions. Here, we annotate all metabolites detected using an untargeted metabolomics approach with a hydrophilic interaction liquid chromatography (HILIC) assay on a Q Exactive HF mass spectrometry.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Blaženović
FIRST_NAME
Ivana
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
WT and ΔSPT cultures of B. thetaiotaomicron and B. ovatus grown BHI liquid media (part I)
STUDY_SUMMARY
Lipid profiling was applied to WT and ΔSPT cultures of B. thetaiotaomicron and B. ovatus grown BHI liquid media revealing a greater variety of Bacteroides-derived sphingolipids than previously recognized, including ceramide phosphoinositol and deoxy-sphingolipids.
INSTITUTE
Broad Institute of MIT and Harvard;Harvard School of Public Health; University of Groningen;Novartis Institute for Biomedical Research Inc Center for the Study of Inflammatory Bowel Disease, University of Groningen and University Medical Center Groningen, Novartis Institute for Biomedical Research Inc
WT and ΔSPT cultures of B. thetaiotaomicron grown in Minimal Media (part II)
STUDY_SUMMARY
Lipid profiling was applied on WT and ΔSPT cultures of B. thetaiotaomicron grown in minimal liquid media in order to confirm the production of Bacteroides-derived sphingolipids.
INSTITUTE
Broad Institute of MIT and Harvard;Harvard School of Public Health; University of Groningen;Novartis Institute for Biomedical Research Inc Center for the Study of Inflammatory Bowel Disease, University of Groningen and University Medical Center Groningen, Novartis Institute for Biomedical Research Inc
Lipid profiling of caecal samples from GF mice colonized with B. thetaiotaomicron WT or the ΔSPT mutants (part III)
STUDY_SUMMARY
To study Bacteroidetes sphingolipids in intestinal health, we colonized germ-free mice with wild type or a sphingolipid-deficient Bacteroides thetaiotaomicron strain. A lack of Bacteroides derived sphingolipids increased intestinal inflammation, dysregulated innate immunity and altered the host ceramide pool.
WT and ΔSPT cultures of B. thetaiotaomicron grown in Minimal Media with or without d4-alanine (part IV)
STUDY_SUMMARY
Lipid profiling was applied on WT and ΔSPT cultures of B. thetaiotaomicron grown in minimal liquid media supplemented with or without deuterium (D4)-labelled alanine, in order to elucidate the production pathways of Bacteroides-derived sphingolipids.
Urea cycle and 1C/serine metabolism in the prevention of oxygen induced retinopathy
STUDY_SUMMARY
Untargeted metabolite profiling links the urea cycle and 1C/serine metabolism in the prevention of oxygen induced retinopathy by hepatic HIF stabilization. Premature infants require oxygen supplementation to survive that is simultaneously toxic to developing tissues. We have demonstrated that hypoxia inducible factor (HIF) stabilization during hyperoxia prevents oxygen induced retinopathy (OIR) and lung disease. Here, untargeted metabolite profiling coupled to XCMS systems biology analysis finds that serine/1C and urea cycles dominate pathway enrichment graphs. MS1 peak areas and MS2 library matches reveal 50% or more increased levels of plasma and retina serine, glycine, hypotaurine, methionine, and taurine. In addition, N-acetylglutamate increased 4-fold in serum, while orotate, citrulline, arginine, aspartate, glutamine were at least 50% increased after HIF stabilization. Targeted data analysis in vivo finds that retinal serine and glycine were derived from liver. HIF-1α2lox/2lox; albumin-cre KO had reduced levels of serine and retinal glycine. Inhibition of 1C metabolism blocked rescue by HIF stabilization. The metabolic phenotype of mice protected from OIR by HIF stabilization is dependent on hepatic serine/1C metabolism and urea cycle.
Presentation of different serum metabolites in trauma patients versus healthy volunteers.
STUDY_SUMMARY
This study seeks to identify critical metabolic differences between patients who have undergone physical trauma and patients who have not experienced physical trauma.
Investigate the False Discovery in Biomarker Research Using LC-HRMS based Untargeted Metabolomics Profiling
STUDY_TYPE
mimicking metabolomics study
STUDY_SUMMARY
Pooled human plasma was spiked separately with two different sets of 11 metabolite standards (22 “true biomarkers”) to mimic plasma samples collected from diseased subjects and non-diseased subjects. Metabolite extracts of individual samples were subjected to biomarker discovery using LC-HRMS.
INSTITUTE
University of Macau, Macau, China
DEPARTMENT
Institute of Translational Medicine, Faculty of Health Sciences,
Downregulation of CENPF epigenetically remodels prostate cancer cells and alters cellular metabolism
STUDY_SUMMARY
This study aimed to determine the metabolic profile of CENPF-knockout (CENPFKO) PC cells and identify differentially expressed metabolites (DEMs) that can be used as diagnostic markers.
INSTITUTE
Cedars-Sinai Medical Center
LAST_NAME
Kim
FIRST_NAME
Jayoung
ADDRESS
8700 Beverly Blvd., Davis 5071 Los Angeles, CA 90048, USA
Different dose exposure of OPC-163493 on HepG2 cells (part-I)
STUDY_TYPE
Compound dosage test
STUDY_SUMMARY
Metabolomics analysis were on 8 samples of HepG2 cells that were treated with compound OPC-163493 (DMSO control, 1, 3, or 10µM; each n=2) exposure for 30 min.
INSTITUTE
Otsuka Pharmaceuticals
LAST_NAME
Kanemoto
FIRST_NAME
Naohide
ADDRESS
463-10 Kagasuno Kawauchi-cho Tokushima 771-0192, Japan
Metabolme analysis of OPC-163493 on the Liver of ZDF rats (part-II)
STUDY_TYPE
Long-term in vivo test
STUDY_SUMMARY
Metabolome analysis were on the 24 samples of ZDF rats that were treated with OPC-163493 for 6-weeks. The 24 samples were composed of 3 different groups (Vehicles, OPC-163493 treatment, and baseline control; each n=8).
INSTITUTE
Otsuka Pharmaceuticals
LAST_NAME
Kanemoto
FIRST_NAME
Naohide
ADDRESS
463-10 Kagasuno Kawauchi-cho Tokushima 771-0192, Japan
Evaluation of metabolome sample preparation and extraction methodologies for oleaginous filamentous fungi Mortierella alpina
STUDY_TYPE
method optimization
STUDY_SUMMARY
In this study, based on the method of fast filtration, we evaluated the three metabolomics analysis protocols commonly used for microbial metabolomics analysis in M. alpina and systematically optimised the metabolite extraction solvent.
INSTITUTE
Jiangnan Unviersity
DEPARTMENT
School of Food Science and Technology
LABORATORY
State Key Laboratory of Food Science and Technology
928 cancer cell lines from 20 major cancer types were cultured in vitro for metabolomic profiling of 124 polar and 101 lipid species. Extracted polar and lipid metabolites were analyzed using hydrophilic interaction
INSTITUTE
Broad Institute of MIT and Harvard
LAST_NAME
Avila
FIRST_NAME
Julian
ADDRESS
415 Main Street, Rm 7175, Cambridge, MA, 02142, USA
Microbial depletion and ozone exposure - Lung tissue (part I)
STUDY_SUMMARY
Global biochemical profiles were determined in lung tissue collected from untreated control mice and mice treated for two weeks with untreated drinking water or water containing an antibiotic cocktail (ampicillin, neomycin, metronidazole, and vancomycin), followed by a three hour exposure to ambient air or ozone (2ppm). Sample collection occurred 24 hours post-ozone exposure.
Microbial depletion and ozone exposure - serum (part II)
STUDY_SUMMARY
Global biochemical profiles were determined in serum collected from untreated control mice and mice treated for two weeks with untreated drinking water or water containing an antibiotic cocktail (ampicillin, neomycin, metronidazole, and vancomycin), followed by a three hour exposure to ambient air or ozone (2ppm). Sample collection occurred 24 hours post-ozone exposure.
Here, we use global metabolomics to differentiate temporal effects (1 – 60 d) found in nonhuman primate (NHP) urine small molecule signatures after a 4 Gy total body irradiation.
INSTITUTE
Georgetown University
LAST_NAME
Pannkuk
FIRST_NAME
Evan
ADDRESS
3970 Reservoir Rd, NW New Research Build, washington dc, District of Columbia, 20057, USA
Here, we use global metabolomics to differentiate temporal effects (1 – 60 d) found in nonhuman primate (NHP) serum small molecule signatures after a 4 Gy total body irradiation.
INSTITUTE
Georgetown University
LAST_NAME
Pannkuk
FIRST_NAME
Evan
ADDRESS
3970 Reservoir Rd, NW New Research Build, washington dc, District of Columbia, 20057, USA
Effect of cell harvesting technique and storage on metabolic profiles in human skin fibroblasts
STUDY_TYPE
Method
STUDY_SUMMARY
Human skin fibroblasts were cultured in MEM media supplemented with 15% FBS. Cells were harvested using (i) trypsinization, (ii) scraping, (iii) methanol fixation and scraping, (iV) methanol fixation, scraping, and drying. Targeted metabolomics analysis of organic acids, amino acids, and acycarnitines was conducted at Mayo Clinic Metabolomics Core Facility.
Metabolomics of a Mouse Model for Retinitis Pigmentosa
STUDY_SUMMARY
Retinitis pigmentosa (RP) is a degenerative disease of the retina that affects approximately 1 million people worldwide. There are multiple genetic causes of this disease, for which, at present, there are no effective therapeutic strategies. We utilized broad spectrum metabolomics to identify perturbations in the metabolism of the rd10 mouse, a genetic model for RP. C57BL/6J and rd10 mice were raised in cyclic light followed by either light or dark adaptation at postnatal day (P) 18, an early stage in the degeneration process. Mice raised entirely in the dark until P18 were also evaluated. After euthanasia, retinas were removed and extracted for analysis by ultra-performance liquid chromatography-time of flight-mass spectrometry (UPLC-QTOF-MS).
4-day dietary effect of fast food vs Mediterranean diet to HDL lipidome
STUDY_TYPE
Dietary intervention study
STUDY_SUMMARY
In this randomized order cross-over study, ten healthy subjects consumed a Mediterranean (Med) and a fast food (FF) diet for 4 days, with a 4-day wash-out between treatments. Lipidomic composition was analyzed in isolated HDL fractions by an untargeted LC-MS method with 15 internal standards. HDL PE content was increased by FF diet, and 41 out of 170 lipid species were differentially affected by diet. Saturated fatty acids (FA) and odd chain FA were enriched after FF diet, while very-long chain FA and unsaturated FA were enriched after Med diet. The composition of PC, TG and CE were significantly altered to reflect the FA composition of the diet whereas the composition of SM and ceramides were generally unaffected, indicating that glycerolipids may be sensitive markers of dietary intake, whereas sphingolipids are more indicative of non-dietary factors. Results from this study indicate that the HDL lipidome is widely remodeled within 4 days of diet change and that certain lipid classes are more sensitive markers of diet whereas other lipid classes are better indicators of non-dietary factors
Metabolomic Analysis of Liver Tissues for Characterization of Hepatocellular Carcinoma
STUDY_SUMMARY
Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer causing more than half a million annual deaths world-wide. Understanding the molecular mechanisms contributing to HCC development and progression is highly desirable for improved surveillance, diagnosis and treatment. Liver tissue metabolomics has the potential to reflect the physiological changes behind HCC development. Also, it allows researchers to investigate racial disparities in HCC. The use of both gas chromatography – mass spectrometry (GC-MS) and liquid chromatography – mass spectrometry (LC-MS) platforms helps increase the metabolome coverage, allowing researchers to better unravel the relationships of metabolites and HCC. The objective of this study is to identify HCC-associated metabolites by analysis of liver tissues from HCC patients using both GC-MS and LC-MS platforms. Paired tumor and non-tumor tissues from 40 patients were analyzed by GC-MS and LC-MS. The patients consist of 14 African-Americans (AA), 10 Asian-Americans (AS), and 16 European-Americans (EA). The levels of the metabolites extracted from the solid liver tissue of the HCC area and adjacent non-HCC area were compared. Among the analytes detected by GC-MS and LC-MS with significant alterations, 17 were selected based on availability of putative metabolite identifications. These metabolites belong to TCA cycle, glycolysis, purines, and lipid metabolism, and have been previously reported in liver metabolomics studies where high correlation with HCC progression was implied. We demonstrated that metabolites that are related to HCC pathogenesis can be identified through metabolomics analysis of liver tissues by both GC-MS and LC-MS. In addition, this analysis has led to the identification of metabolites associated with HCC in a race-specific manner.
Background: Although the erythrocyte is the most abundant cell type in our body, acting as both a deliverer and sensor of oxygen (O2), its function and regulatory mechanism in chronic kidney disease (CKD) remain unknown. Methods: Unbiased metabolomics screening in the whole blood of mice infused with or without angiotensin II (Ang II) at 140ng/kg/min up to 14 days was conducted. Mice with specific ablation of ADORA2B in erythrocytes and patients with CKD were used to determine its function in CKD, potential mechanisms and human relevance. Results: Unbiased metabolomics revealed that 2,3-biphosphoglycerate (2,3-BPG), an erythrocyte-specific metabolite promoting O2 delivery, was significantly induced in an experimental model of CKD induced by Ang II. Mouse genetic studies revealed that erythrocyte ADORA2B signaling via AMPK-stimulated activation of BPG mutase was a key compensatory cellular response to counteract kidney hypoxia, tissue damage and disease progression in Ang II-induced CKD by promoting 2,3-BPG production and O2 delivery. Preclinical studies showed that enhancing AMPK activation offset kidney hypoxia by triggering 2,3-BPG production and O2 delivery. Human translational studies validated mouse findings that erythrocyte 2,3-BPG levels, AMPK activity and O2 delivery capacity were significantly induced in the erythrocytes of CKD patients compared to normal controls and their elevations were correlated to disease severity. Conclusion: Overall, we have provided both mouse and human evidence that ADORA2B-AMPK signaling cascade-induced 2,3-BPG production is a beneficial erythrocyte response to promote O2 delivery to counteract kidney hypoxia and progression of CKD. These findings pave a way to novel therapeutic avenues in CKD.
INSTITUTE
University of Texas Health Science Center McGovern Medical School
A comprehensive plasma metabolomics dataset for a cohort of mouse knockouts within the International Mouse Phenotyping Consortium
STUDY_SUMMARY
Untargeted and targeted metabolomics datasets were acquired for blood plasma samples of 30 mouse knockouts within the International Mouse Phenotyping Consortium (IMPC). http://www.mousephenotype.org/. West Coast Metabolomics Center at UC Davis (https://metabolomics.ucdavis.edu/) conducted the metabolomics analyses.
The Effect of Silicon on Salinity Tolerance and the Associated Metabolomics Profile Changes in Date Palm (part-I)
STUDY_SUMMARY
Silicon has a promising role in the growth and salinity tolerance in plants. While the results obtained from the current study showed that silicon enhanced growth in date palm seedlings, the mechanism behind this observation was also investigated by studying changes occurred in metabolomic profiles triggered by silicon under salinity. The global metabolomic analysis using liquid-chromatography-mass-spectrometry revealed the presence of a number significantly (p ≤ 0.05) accumulated metabolites in leaves and roots when plants were irrigated with silicon and grown under control and salinity conditions.
INSTITUTE
Sultan Qaboos University
DEPARTMENT
Biology
LAST_NAME
Yaish
FIRST_NAME
Mahmoud
ADDRESS
Sultan Qaboos University, Department of Biology, College of Science
Comparative Metabolomic Profiling of Two Contrasting Date Palm Genotypes under Salinity Stress (part-II)
STUDY_SUMMARY
Since metabolites are the net products of the central dogma of cellular biology, this study was aimed to decipher salinity tolerance depends on the information encoded by the metabolomic profiles of the salt tolerant ‘Umsila’ and susceptible ‘Zabad’ cultivars when grown under salinity. Changes in the metabolomic profiles of the leaf and root tissues were determined using hydrophilic interaction liquid chromatography (HILIC) and reverse phase liquid (RPLC) mass spectrometry.
INSTITUTE
Sultan Qaboos University
LAST_NAME
Yaish
FIRST_NAME
Mahmoud
ADDRESS
Department of Biology, College of Science, Sultan Qaboos University
The gut microbiota plays a central role to modulate the plasma metabolome in response to chronic Angiotensin II infusion (part-I)
STUDY_SUMMARY
Six week old C57BL/6 conventional (mice with gut microbiota; conv, n=6) and germ-free (mice without gut microbiota; GF, n=6) mice were infused with angiotensin-II (AngII) for 4 weeks (400ng.kg-1.min-1; Alzet 1004). In parallel control groups, conv (n=6) and GF (n=6) mice received saline via minipumps. Our primary goal was to identify metabolites which were differentially regulated in conventional mice treated with AngII, but not in GF mice, indicating that these metabolites are microbial in origin. Following minipump implantation, animals were housed singly to prevent cross-contamination of microbiota. At the end of fourth week, feces and blood were collected. Both plasma and feces samples were processed and analyzed by using Liquid Chromatography-Tandem Mass Spectroscopy (LC-MS/MS) for metabolite detection (Metabolon).
The gut microbiota plays a central role to modulate the plasma metabolome in response to chronic Angiotensin II infusion (part-II)
STUDY_SUMMARY
Six week old C57BL/6 conventional (mice with gut microbiota; conv, n=6) and germ-free (mice without gut microbiota; GF, n=6) mice were infused with angiotensin-II (AngII) for 4 weeks (400ng.kg-1.min-1; Alzet 1004). In parallel control groups, conv (n=6) and GF (n=6) mice received saline via minipumps. Our primary goal was to identify metabolites which were differentially regulated in conventional mice treated with AngII, but not in GF mice, indicating that these metabolites are microbial in origin. Following minipump implantation, animals were housed singly to prevent cross-contamination of microbiota. At the end of fourth week, feces and blood were collected. Both plasma and feces samples were processed and analyzed by using Liquid Chromatography-Tandem Mass Spectroscopy (LC-MS/MS) for metabolite detection (Metabolon).
Here, we use global metabolomics to differentiate temporal effects (1 – 60 d) found in nonhuman primate (NHP) urine small molecule signatures after a 4 Gy total body irradiation.
Evaluation of computational tools using serial mixtures of human plasma and vegetable juice
STUDY_SUMMARY
Mass spectrometry-based metabolomics is developed rapidly in the past few decades. There are few major vendors for LC-MS platform instruments, for example, Thermo ScientificTM LTQ Orbitrap Velos and Agilent 6510 Q-TOF mass spectrometer were used for metabolomics research. The data acquired cross different platform are rarely compared other than the comparison of the instrument itself on resolution, mass accuracy, sensitivity, dynamic range, scan speed etc., which is largely due to the foundation and principle of the instrument design. Other than this, there are many choice for data preprocessing, i.e., the data acquired from the same platform may have been processed with different feature extraction software tools. The discrepancy for the feature detections with different software will lead to the variation of the down-stream statistics analysis and metabolomics pathway interpretation. In addition, the impact of the LC-MS platform and data preprocessing software tools on the quantitative capabilities is also an interesting topic. In this research, XCMS, mzMine 2.37 and apLCMS are three tools used for the feature extraction of data acquired with Thermo ScientificTM LTQ Orbitrap Velos and Agilent 6510 Q-TOF LC-MS platform by serial dilution experiment. The quantification capability is estimated at the same time based on the linearity, accuracy, and precision
Evaluation of computational tools using serial mixtures of human plasma and vegetable juice (part - II)
STUDY_SUMMARY
Mass spectrometry-based metabolomics is developed rapidly in the past few decades. There are few major vendors for LC-MS platform instruments, for example, Thermo ScientificTM LTQ Orbitrap Velos and Agilent 6510 Q-TOF mass spectrometer were used for metabolomics research. The data acquired cross different platform are rarely compared other than the comparison of the instrument itself on resolution, mass accuracy, sensitivity, dynamic range, scan speed etc., which is largely due to the foundation and principle of the instrument design. Other than this, there are many choice for data preprocessing, i.e., the data acquired from the same platform may have been processed with different feature extraction software tools. The discrepancy for the feature detections with different software will lead to the variation of the down-stream statistics analysis and metabolomics pathway interpretation. In addition, the impact of the LC-MS platform and data preprocessing software tools on the quantitative capabilities is also an interesting topic. In this research, XCMS, mzMine 2.37 and apLCMS are three tools used for the feature extraction of data acquired with Thermo ScientificTM LTQ Orbitrap Velos and Agilent 6510 Q-TOF LC-MS platform by serial dilution experiment. The quantification capability is estimated at the same time based on the linearity, accuracy, and precision.
Variability in metabolomic profiles among unique genotypes of Acropora cervicornis (part-II)
STUDY_SUMMARY
We hypothesized that each of the three genotypes tested would have unique metabolomic profiles. These data increase our basic knowledge of the coral metabolome and represent an important step toward linking genotype, phenotype, and metabolome in reef-building corals.
Physiological and metabolic response of crab megalopae and juveniles to ocean acidification (part-III)
STUDY_SUMMARY
Young crab samples were placed into 1 of 4 treatment groups to understand their metabolic response to ocean acidification and dissolved oxygen content.
Comprehensive Profiling by Non-targeted Stable Isotope Tracing Capillary Electrophoresis-Mass Spectrometry
STUDY_SUMMARY
We developed a stable-isotope tracing capillary electrophoresis (CE)-MS metabolomics approach to cover polar metabolites as well as isotopologues in a non-targeted way. An in-house developed software enables high throughput processing of complex multi-dimensional data. The practicability is demonstrated analysing 13C-U-glucose exposed prostate cancer and non-cancer cells.
INSTITUTE
Dalian Institute Of Chemical Physics, Chinese Academy Of Sciences
LAST_NAME
Wang
FIRST_NAME
Zhichao
ADDRESS
457, Zhongshan Road
EMAIL
wangzc05@dicp.ac.cn
PHONE
+86-15998625250
STUDY_COMMENTS
Comprehensive Profiling by Non-targeted Stable Isotope Tracing Capillary Electrophoresis-Mass Spectrometry - A Novel Tool Complementing Metabolomics Analyses of Polar Metabolites
Alterations in fecal metabolic patterns are associated with atrial fibrillation
STUDY_SUMMARY
Little evidence has been reported in characterizing the fecal alterations in metabolic patterns in atrial fibrillation (AF). We include the result of the global alterations that occur in the intestinal microbiota in a cohort of AF patients and matched controls based on a strategy of metabolomic analyses. Our findings characterize the disordered microbial metabolite profiles in AF.
Alterations in serum metabolic patterns are associated with atrial fibrillation
STUDY_SUMMARY
Little evidence has been reported in characterizing the serum alterations in metabolic patterns in atrial fibrillation (AF). We include the result of the global alterations that occur in the intestinal microbiota in a cohort of AF patients and matched controls based on a strategy of metabolomic analyses. Our findings characterize the disordered microbial metabolite profiles in AF.
Deep Metabolomics of a High-Grade Serous Ovarian Cancer Triple Knockout Mouse Model.
STUDY_TYPE
Untargeted metabolomics
STUDY_SUMMARY
Metabolic alternations were investigated by applying Ultra Performance Liquid Chromatography Mass Spectrometry (UPLC-MS) to serum samples collected from triple knockout (TKO) mice at pre-malignant, early, and advanced stages of HGSC. Samples were analyzed with control mice, which have the same genetic background as TKO mice but develop no tumors. To enhance the selectivity for HGSC-specific metabolite markers, a tumor control group was also included. These were uterine tumor (UT) mice that developed uterine tumors, but no HGSC. All samples were analyzed using reverse phase (RP) and hydrophilic interaction liquid chromatography (HILIC) UPLC-MS analysis in positive and negative ion modes.
Combinatorial metabolic mixtures for encoding abstract digital data
STUDY_TYPE
MALDI MS
STUDY_SUMMARY
We present several kilobyte-scale image datasets stored in synthetic metabolomes, which are decoded with accuracy exceeding 98-99% using multi-mass logistic regression.
INSTITUTE
Brown University
DEPARTMENT
Engineering
LABORATORY
Rosenstein Lab
LAST_NAME
Kennedy
FIRST_NAME
Eamonn
ADDRESS
Barus & Holley room 353, 184 Hope St
EMAIL
eamonn_kennedy@brown.edu
PHONE
7737507192
PUBLICATIONS
E. Kennedy et al. “Encoding information in synthetic metabolomes” Plos One, accepted, 2019
Analysis of short chain phosphatidylcholine (PC) on the Golgi membrane
STUDY_TYPE
Golgi membrane lipids characterization
STUDY_SUMMARY
Studies on vesicle formation by the Coat Protein I (COPI) complex have contributed to a basic understanding of how vesicular transport is initiated. We have identified that short chain lipids promote membrane properties that are conducive for fission. Here we investigated short chain PCs on Golgi membrane. These findings will advance the understanding of how lipid geometry contributes to membrane deformation needed for vesicle fission.
Metabolomic analysis of C2C12 myoblasts induced by the transcriptional factor FOXO1
STUDY_SUMMARY
The transcriptional factor FOXO1 is considered to play roles in the regulation of energy metabolism in various tissues. To determine the metabolic changes occurring due to the activation of FOXO1, we analyzed the metabolic profile of C2C12 myoblasts expressing FOXO1-estrogen receptor fusion protein using CE-TOFMS. In the FOXO1-activated cells, the metabolite levels during glycolysis were higher. In addition, the gene expression of pyruvate dehydrogenase kinase, an enzyme that inhibits glucose utilization, increased. In the FOXO1-activated cells, the metabolite levels of numerous amino acids decreased, with increased gene expression of branched chain amino acid metabolism enzymes. Our results suggest that FOXO1 suppresses glucose utilization and promotes the use of proteins/amino acids as energy sources in muscle cells, potentially during starvation.
INSTITUTE
Kyoto Prefectural University
LAST_NAME
Kamei
FIRST_NAME
Yasutomi
ADDRESS
1-5 Hangi-cho, Shimogamo, Sakyo-ku Kyoto, Kyoto, Kyoto, 606-8522, Japan
Metabolomic analysis of skeletal muscle in young and aged mice
STUDY_SUMMARY
Sarcopenia is the age-induced, progressive loss of skeletal muscle mass and function, which results in poor muscle performance. To better understand changes in skeletal muscles during sarcopenia, we performed a metabolomic analysis of skeletal muscle in young (8-week-old) and aged (28-month-old) mice using CE-TOFMS. Our data shows that the metabolites including glucose and polyamine metabolism were decreased in aged mice compared with young mice. In addition, neurotransmitter levels were higher in aged mice.
INSTITUTE
Kyoto Prefectural University
LAST_NAME
Kamei
FIRST_NAME
Yasutomi
ADDRESS
1-5 Hangi-cho, Shimogamo, Sakyo-ku Kyoto, Kyoto, Kyoto, 606-8522, Japan
Metabolome Profiling of Synechococcus elogatus PCC 11802
STUDY_TYPE
Quantitative Metabolomics
STUDY_SUMMARY
Metabolomics Analysis of a novel freshwater cyanobacterium, Synechococcus elongatus PCC 11802 isolated by us from Powai Lake, Mumbai, India. PCC 11802 cells were grown under ambient and 1% CO2 conditions and metabolomics data was collected in three biological replicates and two technical replicates (n=6). The study aims to find metabolomics changes in this cyanobacterium at elevated CO2 levels.
Genetic and metabolic characterization of bioengineered human fatty liver tissue with modified SIRT1 expression
STUDY_SUMMARY
Lipidomics and metabolomics was performed three types of tissue samples to compare human normal liver tissue against human NASH liver and the bioengineered human iPS-derived fatty liver tissue-iKD-SIRT1. The purpose of this study was to show that the global lipidomics profile of iPS-derived fatty liver tissue-iKD-SIRT1 was similar to that of patients with NASH
INSTITUTE
University of Pittsburgh
DEPARTMENT
Department of Pathology
LAST_NAME
Soto-Gutierrez
FIRST_NAME
Alejandro
ADDRESS
200 Lothrop Street, 423 Biomedical Science Tower, Pittsburgh, PA 15261, USA
Untargeted metabolomics on control and compound-treated STHdhQ111 cells and control STHdhQ7 cells
STUDY_SUMMARY
Cells expressing mutant huntingtin were treated in triplicate with serum-free DMEM with vehicle (Q111SST) or serum-free DMEM with one of 14 protective compounds for 24 hours. Wild type cells were also treated with serum-free DMEM with vehicle (Q7SST) as an additional control for 24 hours. We examined the compounds' metabolomic effects on the cells using untargeted mass spectrometry, which measured lipids and polar metabolites.
Effects of selenate and cadmium exposure on the honey bee metabolome
STUDY_SUMMARY
We moved one frame of brood each from five healthy honey bee colonies with marked Italian queens and housed them in a hive body at 35°C and 50% humidity under constant darkness. We then allowed the bees to emerge, mixed the newly emerged workers (NEWs) to randomize their colony of origin and placed NEWs into 13 cm x 10.5 cm x 6.5 cm wire cages equipped with feeders containing 35mL of deionized water and 35mL 50% sucrose. We also provided a pollen patty to each cage of bees consisting of 269g corn syrup, 113g sucrose and 113g of Bee Pro (Mann Lake, Hackensack, MN). To inoculate the newly emerged workers with their “core” microbiome, we collected 50 mL of foragers from the source hives of the NEWs, immobilized the bees at 4°C, aseptically dissected out the abdomens and macerated the whole abdomens in 50% sucrose. We added 1 mL of the resulting slurry to 34 mL of 50% sucrose solution and fed it to the NEWs. We allowed the bees to feed ad libitium on the mixture for two days before replacing the feeders with 50% sucrose. We allowed the bees to feed for three more days to fully establish a microbiome. Once the bees had an established microbiome, we prepared treatment feeding solutions of 50% sucrose (as a no metal/metalloid control), 50% sucrose spiked with 0.6 mg/L sodium selenate or 50% sucrose with 0.24 mg/L cadmium chloride (Alfa Aesar, Ward Hill, MA) and pollen patties spiked with either 6.0 mg/L selenium or 0.46 mg/L cadmium as in Hladun et al 2015. We again allowed the bees to feed ad libitium. We sampled three bees from 13 cages after four days of continuous exposure to the above-mentioned treatments and immediately placed the samples on dry ice, followed by long-term storage at -80 °C.
Metabolite profiling across the 1st and 2nd intraerythrocytic developmental lifecycles of the malaria parasite P. falciparum following induction of delayed death with indolmycin treatment
A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research
STUDY_TYPE
Stool metabolite profiling
STUDY_SUMMARY
Fecal microbiota transplantation (FMT) is used in the treatment of microbiome-associated diseases such as Clostridium difficile infections. In order to develop synthetic therapeutics and customized disease treatments we will need to understand the bacterial communities in the stool samples used in such treatments. For this purpose, a microbiome library was generated using human stool obtained from healthy human FMT recruited by OpenBiome, a non-profit organization that provides fecal microbiome therapeutics. In addition to characterizing the bacterial populations and obtaining bacterial isolates from FMT samples, we conducted metabolite profiling with the goal of: (1) generating a library of metabolites in FMT samples, (2) Identifying metabolites associated with defined bacterial populations, and (3) identifying microbial metabolites with immunoregulatory functions. We conducted metabolite profiling on a subset consisting of 180 stool samples from 84 donors using four nontargeted liquid chromatography mass spectrometry (LC-MS) methods. Generated data were processed, isotopes removed, and adducts and fragments clustered. The identity of known metabolites was determined based on matching retention times of neat standards run in parallel with the study.
Flavonoid study of Ginkgo leaves facing to different elevation and plant age
STUDY_SUMMARY
Ginkgo biloba leaves are always resources for flavonoids pharmaceutical industry. Thus, artificial planting and industrial harvesting become the vital aspect to get higher drug yields. In this research, we performed de novo transcriptome sequencing of Ginkgo leaves coupled with high-performance liquid chromatography/quadrupole-time-of-flight mass spectrometry analyses to obtain a comprehensive understanding of the influence of elevation and plant age on flavonoid synthesis. A total of 557,659,530 clean reads were assembled into 188,155 unigenes, of which 135,102 (71.80%) were successfully annotated in seven public databases. The differentially expressed genes analysis indicated DFR, LAR and ANR were significantly up-regulated with the increase of elevation in young Ginkgo trees leaves. With less strict saliency, the relative concentration of flavonoid derivatives with high parent ion signal intensity was likely to support this conclusion. Complex gene variations were observed with the plant age change. However, flavonoid derivatives analysis predicted the potential possibility that the rise of plant age is more likely to be detrimental to the biosynthesis of Ginkgo flavonoids in leaves. From the overall DEGs involved in flavonoid biosynthesis, DFRs seemed to show more considerable variability towards the variation of elevation and plant age. Furthermore, our research effectively expanded the functional genomic library of Ginkgo and provided a reference for artificial planting and industrial harvesting.
INSTITUTE
Central South University, China
LAST_NAME
Zou
FIRST_NAME
Kai
ADDRESS
Central South University, 932 Lushan South Road, Yuelu District, Changsha City, Hunan Province
Non-targeted GC-MS Analysis of Polar Soluble Fraction (part-I)
STUDY_SUMMARY
Cyanobacteria are a model photoautotroph and a chassis for the sustainable production of fuels and chemicals. Yet, knowledge of photoautotrophic metabolism in the natural environment of day/night cycles is lacking yet has implications for improved yield from plants, algae, and cyanobacteria. Here, a thorough approach to characterizing diverse metabolites—including carbohydrates, lipids, amino acids, pigments, co-factors, nucleic acids and polysaccharides—in the model cyanobacterium Synechocystis sp. PCC 6803 (S. 6803) under sinusoidal diurnal light-dark cycles was developed and applied. A custom photobioreactor and novel multi-platform mass spectrometry workflow enabled metabolite profiling every 30-120 minutes across a 24-hour diurnal sinusoidal LD (“sinLD”) cycle peaking at 1,600 mol photons m 2 s-1. We report widespread oscillations across the sinLD cycle with 90%, 94%, and 40% of the identified polar/semi-polar, non-polar, and polymeric metabolites displaying statistically significant oscillations, respectively. Microbial growth displayed distinct lag, biomass accumulation, and cell division phases of growth. During the lag phase, amino acids (AA) and nucleic acids (NA) accumulated to high levels per cell followed by decreased levels during the biomass accumulation phase, presumably due to protein and DNA synthesis. Insoluble carbohydrates displayed sharp oscillations per cell at the day-to-night transition. Potential bottlenecks in central carbon metabolism are highlighted. Together, this report provides a comprehensive view of photosynthetic metabolite behavior with high temporal resolution, offering insight into the impact of growth synchronization to light cycles via circadian rhythms. Incorporation into computational modeling and metabolic engineering efforts promises to improve industrially-relevant strain design.
Non-targeted GC-MS Analysis of Insoluble Metabolites (part-II)
STUDY_SUMMARY
Cyanobacteria are a model photoautotroph and a chassis for the sustainable production of fuels and chemicals. Yet, knowledge of photoautotrophic metabolism in the natural environment of day/night cycles is lacking yet has implications for improved yield from plants, algae, and cyanobacteria. Here, a thorough approach to characterizing diverse metabolites—including carbohydrates, lipids, amino acids, pigments, co-factors, nucleic acids and polysaccharides—in the model cyanobacterium Synechocystis sp. PCC 6803 (S. 6803) under sinusoidal diurnal light-dark cycles was developed and applied. A custom photobioreactor and novel multi-platform mass spectrometry workflow enabled metabolite profiling every 30-120 minutes across a 24-hour diurnal sinusoidal LD (“sinLD”) cycle peaking at 1,600 ?mol photons m 2 s-1. We report widespread oscillations across the sinLD cycle with 90%, 94%, and 40% of the identified polar/semi-polar, non-polar, and polymeric metabolites displaying statistically significant oscillations, respectively. Microbial growth displayed distinct lag, biomass accumulation, and cell division phases of growth. During the lag phase, amino acids (AA) and nucleic acids (NA) accumulated to high levels per cell followed by decreased levels during the biomass accumulation phase, presumably due to protein and DNA synthesis. Insoluble carbohydrates displayed sharp oscillations per cell at the day-to-night transition. Potential bottlenecks in central carbon metabolism are highlighted. Together, this report provides a comprehensive view of photosynthetic metabolite behavior with high temporal resolution, offering insight into the impact of growth synchronization to light cycles via circadian rhythms. Incorporation into computational modeling and metabolic engineering efforts promises to improve industrially-relevant strain design.
Non-targeted LC-MS Analysis of Soluble Metabolites in the Non-Polar MTBE Phase (part-V)
STUDY_SUMMARY
Cyanobacteria are a model photoautotroph and a chassis for the sustainable production of fuels and chemicals. Yet, knowledge of photoautotrophic metabolism in the natural environment of day/night cycles is lacking yet has implications for improved yield from plants, algae, and cyanobacteria. Here, a thorough approach to characterizing diverse metabolites—including carbohydrates, lipids, amino acids, pigments, co-factors, nucleic acids and polysaccharides—in the model cyanobacterium Synechocystis sp. PCC 6803 (S. 6803) under sinusoidal diurnal light-dark cycles was developed and applied. A custom photobioreactor and novel multi-platform mass spectrometry workflow enabled metabolite profiling every 30-120 minutes across a 24-hour diurnal sinusoidal LD (“sinLD”) cycle peaking at 1,600 mol photons m 2 s-1. We report widespread oscillations across the sinLD cycle with 90%, 94%, and 40% of the identified polar/semi-polar, non-polar, and polymeric metabolites displaying statistically significant oscillations, respectively. Microbial growth displayed distinct lag, biomass accumulation, and cell division phases of growth. During the lag phase, amino acids (AA) and nucleic acids (NA) accumulated to high levels per cell followed by decreased levels during the biomass accumulation phase, presumably due to protein and DNA synthesis. Insoluble carbohydrates displayed sharp oscillations per cell at the day-to-night transition. Potential bottlenecks in central carbon metabolism are highlighted. Together, this report provides a comprehensive view of photosynthetic metabolite behavior with high temporal resolution, offering insight into the impact of growth synchronization to light cycles via circadian rhythms. Incorporation into computational modeling and metabolic engineering efforts promises to improve industrially-relevant strain design.
Peroxide antimalarial extended treatment timecourse on trophozoite-stage P. falciparum parasites
STUDY_SUMMARY
Red blood cells (RBCs) infected with trophozoite stage P. falciparum parasites (3D7 strain) at 10% parasitaemia and 2% haematocrit were treated with OZ277 (300 nM), OZ439 (300 nM), DHA (100 nM) or vehicle (0.03% DMSO). This was a 4-timepoint study, with samples taken 0, 3, 6 and 9 h after drug or vehicle addition. Samples treated with vehicle acted as the untreated control. Samples from drug treated uninfected RBCs were also taken to ensure the observed drug effects were parasite specific.
INSTITUTE
Monash University
LAST_NAME
Giannangelo
FIRST_NAME
Carlo
ADDRESS
381 Royal Parade, Parkville, Victoria, 3052, Australia
Peroxide antimalarial treatment of K13-mutant and -wildtype P. falciparum parasites
STUDY_SUMMARY
Red blood cells (RBCs) infected with trophozoite stage P. falciparum parasites (Cam3.IIR539T or Cam3.IIrev lines) at 4% parasitaemia and 2% haematocrit were treated with 100 nM of DHA, OZ277 or OZ439 for a duration of 1, 3 and 5 h, respectively. The K13-mutant artemisinin resistant parasite line used was Cam3.IIR539T. The K13-wildtype artemisinin sensitive parasite line used was Cam3.IIrev. The Samples treated with vehicle (DMSO) acted as the untreated control.
INSTITUTE
Monash University
LAST_NAME
Giannangelo
FIRST_NAME
Carlo
ADDRESS
381 Royal Parade, Parkville, Victoria, 3052, Australia
Characterization of feces in Atrial Fibrillation (AF) patients
STUDY_SUMMARY
Atrial Fibrillation (AF), an abnormal heart rhythm characterized by the rapid and irregular beating of the atria, is the most common arrhythmia with heavy global burdens. The present project aimed to characterized the feature of metabolites in feces of AF patients by using LC-MS.
Metabolomic Markers of Methotrexate Response, In Vitro
STUDY_SUMMARY
Erythroblastoid cells (K562) maintained in logarithmic growth phase were treated with 1000 nM methotrexate or vehicle alone (i.e. D-PBS) under standard culture conditions for 24 hours. Cellular response to methotrexate was measured based on anti-proliferative activity by cell counting. Cells were washed, flash frozen in liquid nitrogen and submitted for metabolomics analysis to the NIH West Coast Metabolomics Center.
Fish-oil supplementation in pregnancy, child metabolomics and asthma risk
STUDY_SUMMARY
We investigated potential metabolic mechanisms using untargeted liquid chromatography-mass spectrometry-based metabolomics on 577 plasma samples collected at age 6 months in the offspring of mothers participating in the n-3 LCPUFA randomized controlled trial. First, associations between the n-3 LCPUFA supplementation groups and child metabolite levels were investigated using univariate regression models and data-driven partial least square discriminant analyses (PLS-DA). Second, we analyzed the association between the n-3 LCPUFA metabolomic profile and asthma development using Cox-regression. Third, we conducted mediation analyses to investigate whether the protective effect of n-3 LCPUFA on asthma was mediated via the metabolome
INSTITUTE
Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen
DEPARTMENT
Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital
Serum lipidomic profile of cold-exposed Ucp1cre/12-LOX KO mice
STUDY_SUMMARY
We aimed to evaluate whether specific deletion of 12-Lipoxygenase (12-LOX) in brown fat can affect the serum concentrations of 12-LOX products under cold exposure.
We aimed to determine the levels of the cold-induced 12-LOX products in patients with different degrees of body mass index (BMI). This analysis allowed us to infer about the role of these oxylipins in the pathophysiology of obesity.
Effects of selenate and cadmium exposure on the honey bee metabolome
STUDY_SUMMARY
We moved one frame of brood each from five healthy honey bee colonies with marked Italian queens and housed them in a hive body at 35°C and 50% humidity under constant darkness. We then allowed the bees to emerge, mixed the newly emerged workers (NEWs) to randomize their colony of origin and placed NEWs into 13 cm x 10.5 cm x 6.5 cm wire cages equipped with feeders containing 35mL of deionized water and 35mL 50% sucrose. We also provided a pollen patty to each cage of bees consisting of 269g corn syrup, 113g sucrose and 113g of Bee Pro (Mann Lake, Hackensack, MN). To inoculate the newly emerged workers with their “core” microbiome, we collected 50 mL of foragers from the source hives of the NEWs, immobilized the bees at 4°C, aseptically dissected out the abdomens and macerated the whole abdomens in 50% sucrose. We added 1 mL of the resulting slurry to 34 mL of 50% sucrose solution and fed it to the NEWs. We allowed the bees to feed ad libitium on the mixture for two days before replacing the feeders with 50% sucrose. We allowed the bees to feed for three more days to fully establish a microbiome. Once the bees had an established microbiome, we prepared treatment feeding solutions of 50% sucrose (as a no metal/metalloid control), 50% sucrose spiked with 0.6 mg/L sodium selenate or 50% sucrose with 0.24 mg/L cadmium chloride (Alfa Aesar, Ward Hill, MA) and pollen patties spiked with either 6.0 mg/L selenium or 0.46 mg/L cadmium as in Hladun et al 2015. We again allowed the bees to feed ad libitium. We sampled three bees from 13 cages after four days of continuous exposure to the above-mentioned treatments and immediately placed the samples on dry ice, followed by long-term storage at -80 °C.
Lyme disease is a tick-borne bacterial illness that occurs in areas of North America, Europe, and Asia. Early infection typically presents as generalized symptoms with an erythema migrans (EM) skin lesion. Bacterial dissemination can result in multiple EM skin lesions or in extracutaneous manifestations such as Lyme neuroborreliosis. Metabolic biosignatures of patients with early Lyme disease can potentially provide diagnostic targets, as well as highlight metabolic pathways that contribute to pathogenesis. Sera from well-characterized patients diagnosed with either early localized Lyme disease (ELL) or early disseminated Lyme disease (EDL), plus healthy individuals (HC), from the United States were analyzed by liquid chromatography-mass spectrometry (LC-MS). Comparative analyses were performed between ELL, or EDL, or ELL combined with EDL, and the HC to develop biosignatures present in early Lyme disease. A direct comparison between ELL and EDL was also performed to develop a biosignature for stages of early Lyme disease. Metabolic pathway analysis and chemical identification of metabolites with LC-tandem mass spectrometry (LC-MS/MS) demonstrated alterations of eicosanoid, bile acid, sphingolipid, glycerophospholipid, and acylcarnitine metabolic pathways during early Lyme disease . These metabolic alterations were confirmed using a separate set of serum samples for validation. The findings demonstrated the metabolic pathways altered in the host during early Lyme disease and provide evidence that the diversity in the type of early Lyme disease manifestations may be associated with particular metabolic alterations.
INSTITUTE
Colorado State University
DEPARTMENT
MIP
LABORATORY
Belisle
LAST_NAME
Belisle
FIRST_NAME
John
ADDRESS
200 West Lake, Campus Delivery 0922, Colorado State University, Fort Collins, CO, 80523
Vaginal swab lipidome profiles at 48 h reflect the fat composition of neonatal diet during first two days postnatal
STUDY_TYPE
MRM-profiling
STUDY_SUMMARY
In this study, we further investigated the efficacy of using MRM-profiling of vaginal lipids to differentiate PND 2 vaginal swabs between gilts suckled by sow or fed milk replacer. Secondly, we tested the effect of a lard based supplement on vaginal lipid profiles of gilts.
INSTITUTE
Purdue University
DEPARTMENT
Animal Sciences
LABORATORY
Metabolite Profiling Facility - Purdue University
LAST_NAME
Ferreira
FIRST_NAME
Christina
ADDRESS
1203 W. State St, West Lafayette, IN, 47906, USA
EMAIL
cferrei@purdue.edu
PHONE
7654095924
NUM_GROUPS
colostrum suckled (S, n=8); S plus fat supplement (SF, n=5); bottle-fed milk replacer (B, n=8); or B plus fat supplement (BF, n=7
We propose to evaluate microbial and metabolic profiles in baseline and endpoint colonic mucosal, fecal, and serum samples from human patients at risk for CRC and enrolled in a 90-day phase I clinical trial. Patients will receive daily supplementation with calcium alone, a calcium-rich multimineral (Aquamin?), or placebo (maltodextrin) (n=10 per group). We hypothesize that dietary supplementation will correlate with CRC-protective metabolic profiles and that multimineral supplementation will generate more favorable profiles than calcium supplementation alone.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
Ann Arbor, MI
EMAIL
mkachman@med.umich.edu
PHONE
734-232-0842
NUM_GROUPS
24
TOTAL_SUBJECTS
18
STUDY_COMMENTS
Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer related death when both genders are combined. Epidemiologically, calcium intake has been protective against colonic adenomas and even colon cancer. Calcium supplementation has reduced the risk of colon adenoma formation in subjects with a history of previous colon polyps. The utility of calcium supplementation for colon cancer prevention is somewhat modulated by the modest or inconsistent level of protection afforded. Our preliminary data in mice and human enterocyte models shows that dietary supplementation with a multimineral supplement (Aquamin?) containing calcium in combination with 72 measureable trace minerals is more protective against tumors and epithelial growth dysregulation than calcium alone. One potential mechanism, supported by our rodent data, is that multimineral supplementation alters gut microbial populations to generate bile acid and short chain fatty acid (SCFA) profiles that are CRC-protective.
We propose to evaluate microbial and metabolic profiles in baseline and endpoint colonic mucosal, fecal, and serum samples from human patients at risk for CRC and enrolled in a 90-day phase I clinical trial. Patients will receive daily supplementation with calcium alone, a calcium-rich multimineral (Aquamin?), or placebo (maltodextrin) (n=10 per group). We hypothesize that dietary supplementation will correlate with CRC-protective metabolic profiles and that multimineral supplementation will generate more favorable profiles than calcium supplementation alone.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
Ann Arbor, MI
EMAIL
mkachman@med.umich.edu
PHONE
734-232-0842
NUM_GROUPS
24
TOTAL_SUBJECTS
18
STUDY_COMMENTS
Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer related death when both genders are combined. Epidemiologically, calcium intake has been protective against colonic adenomas and even colon cancer. Calcium supplementation has reduced the risk of colon adenoma formation in subjects with a history of previous colon polyps. The utility of calcium supplementation for colon cancer prevention is somewhat modulated by the modest or inconsistent level of protection afforded. Our preliminary data in mice and human enterocyte models shows that dietary supplementation with a multimineral supplement (Aquamin?) containing calcium in combination with 72 measureable trace minerals is more protective against tumors and epithelial growth dysregulation than calcium alone. One potential mechanism, supported by our rodent data, is that multimineral supplementation alters gut microbial populations to generate bile acid and short chain fatty acid (SCFA) profiles that are CRC-protective.
We propose to evaluate microbial and metabolic profiles in baseline and endpoint colonic mucosal, fecal, and serum samples from human patients at risk for CRC and enrolled in a 90-day phase I clinical trial. Patients will receive daily supplementation with calcium alone, a calcium-rich multimineral (Aquamin?), or placebo (maltodextrin) (n=10 per group). We hypothesize that dietary supplementation will correlate with CRC-protective metabolic profiles and that multimineral supplementation will generate more favorable profiles than calcium supplementation alone.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
Ann Arbor, MI
EMAIL
mkachman@med.umich.edu
PHONE
734-232-0842
NUM_GROUPS
24
TOTAL_SUBJECTS
18
STUDY_COMMENTS
Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer related death when both genders are combined. Epidemiologically, calcium intake has been protective against colonic adenomas and even colon cancer. Calcium supplementation has reduced the risk of colon adenoma formation in subjects with a history of previous colon polyps. The utility of calcium supplementation for colon cancer prevention is somewhat modulated by the modest or inconsistent level of protection afforded. Our preliminary data in mice and human enterocyte models shows that dietary supplementation with a multimineral supplement (Aquamin?) containing calcium in combination with 72 measureable trace minerals is more protective against tumors and epithelial growth dysregulation than calcium alone. One potential mechanism, supported by our rodent data, is that multimineral supplementation alters gut microbial populations to generate bile acid and short chain fatty acid (SCFA) profiles that are CRC-protective.
We propose to evaluate microbial and metabolic profiles in baseline and endpoint colonic mucosal, fecal, and serum samples from human patients at risk for CRC and enrolled in a 90-day phase I clinical trial. Patients will receive daily supplementation with calcium alone, a calcium-rich multimineral (Aquamin?), or placebo (maltodextrin) (n=10 per group). We hypothesize that dietary supplementation will correlate with CRC-protective metabolic profiles and that multimineral supplementation will generate more favorable profiles than calcium supplementation alone.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
Ann Arbor, MI
EMAIL
mkachman@med.umich.edu
PHONE
734-232-0842
NUM_GROUPS
24
TOTAL_SUBJECTS
18
STUDY_COMMENTS
Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer related death when both genders are combined. Epidemiologically, calcium intake has been protective against colonic adenomas and even colon cancer. Calcium supplementation has reduced the risk of colon adenoma formation in subjects with a history of previous colon polyps. The utility of calcium supplementation for colon cancer prevention is somewhat modulated by the modest or inconsistent level of protection afforded. Our preliminary data in mice and human enterocyte models shows that dietary supplementation with a multimineral supplement (Aquamin?) containing calcium in combination with 72 measureable trace minerals is more protective against tumors and epithelial growth dysregulation than calcium alone. One potential mechanism, supported by our rodent data, is that multimineral supplementation alters gut microbial populations to generate bile acid and short chain fatty acid (SCFA) profiles that are CRC-protective.
We propose to evaluate microbial and metabolic profiles in baseline and endpoint colonic mucosal, fecal, and serum samples from human patients at risk for CRC and enrolled in a 90-day phase I clinical trial. Patients will receive daily supplementation with calcium alone, a calcium-rich multimineral (Aquamin?), or placebo (maltodextrin) (n=10 per group). We hypothesize that dietary supplementation will correlate with CRC-protective metabolic profiles and that multimineral supplementation will generate more favorable profiles than calcium supplementation alone.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
Ann Arbor, MI
EMAIL
mkachman@med.umich.edu
PHONE
734-232-0842
NUM_GROUPS
24
TOTAL_SUBJECTS
18
STUDY_COMMENTS
Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer related death when both genders are combined. Epidemiologically, calcium intake has been protective against colonic adenomas and even colon cancer. Calcium supplementation has reduced the risk of colon adenoma formation in subjects with a history of previous colon polyps. The utility of calcium supplementation for colon cancer prevention is somewhat modulated by the modest or inconsistent level of protection afforded. Our preliminary data in mice and human enterocyte models shows that dietary supplementation with a multimineral supplement (Aquamin?) containing calcium in combination with 72 measureable trace minerals is more protective against tumors and epithelial growth dysregulation than calcium alone. One potential mechanism, supported by our rodent data, is that multimineral supplementation alters gut microbial populations to generate bile acid and short chain fatty acid (SCFA) profiles that are CRC-protective.
Plasma untargeted metabolomics study of pulmonary tuberculosis
STUDY_SUMMARY
In this study, differentially abundant plasma metabolites were screened by using the ultra-high performance liquid chromatography coupled with Q Exactive mass spectrometry in pulmonary tuberculosis(TB) patients and normal controls(NC) or patients with other pulmonary diseases such as, community-acquired pneumonia(CAP) and lung cancer(LC).
INSTITUTE
Zhengjiang University
DEPARTMENT
School of Medicine
LABORATORY
Institute of Cell Biology
LAST_NAME
Li
FIRST_NAME
Ji-Cheng
ADDRESS
866 Yuhangtang Road, West Lake District, Hangzhou, Zhejiang Province, 310058, PR China
Metabolic responses to PD1 immune-checkpoint blockade and association with therapeutic benefits - Part I
STUDY_SUMMARY
Inhibition of immune-checkpoint targets including PD1 is clinically effective in a variety of cancers. However, only a subset of patients respond and complete response remains uncommon. Given the known role of metabolites in modulating immunity, we sought to understand how individual patients’ metabolic activities adapt to PD1 immune checkpoint blockade and how they associate with therapeutic benefits. To this end, we profiled metabolites in pre- and multiple on-treatment patient serum samples from three independent immunotherapy trials using hydrophilic interaction liquid chromatography coupled with either triple quadrupole MS multiple reaction monitoring or high resolution full scan MS detection. The study consisted of two Phase I trials (CA209-038, NCT01621490; CA209-009, NCT01358721) which included 78 patients with advanced melanoma and 91 patients with metastatic renal cell carcinoma (RCC) treated with nivolumab. To investigate the generalizability of our results, we also analyzed a large randomized Phase III trial (CheckMate 025, NCT01668784) with 743 RCC patients, among which 394 received nivolumab and 349 received everolimus. V600E is the most common BRAF mutation in melanoma and "BRAF_V600E" indicates the mutation status.
Metabolic responses to PD1 immune-checkpoint blockade and association with therapeutic benefits - Part II
STUDY_SUMMARY
Inhibition of immune-checkpoint targets including PD1 is clinically effective in a variety of cancers. However, only a subset of patients respond and complete response remains uncommon. Given the known role of metabolites in modulating immunity, we sought to understand how individual patients’ metabolic activities adapt to PD1 immune checkpoint blockade and how they associate with therapeutic benefits. To this end, we profiled metabolites in pre- and multiple on-treatment patient serum samples from three independent immunotherapy trials using hydrophilic interaction liquid chromatography coupled with either triple quadrupole MS multiple reaction monitoring or high resolution full scan MS detection. The study consisted of two Phase I trials (CA209-038, NCT01621490; CA209-009, NCT01358721) which included 78 patients with advanced melanoma and 91 patients with metastatic renal cell carcinoma (RCC) treated with nivolumab. To investigate the generalizability of our results, we also analyzed a large randomized Phase III trial (CheckMate 025, NCT01668784) with 743 RCC patients, among which 394 received nivolumab and 349 received everolimus. V600E is the most common BRAF mutation in melanoma and "BRAF_V600E" indicates the mutation status.
Metabolic responses to PD1 immune-checkpoint blockade and association with therapeutic benefits - Part III
STUDY_SUMMARY
Inhibition of immune-checkpoint targets including PD1 is clinically effective in a variety of cancers. However, only a subset of patients respond and complete response remains uncommon. Given the known role of metabolites in modulating immunity, we sought to understand how individual patients’ metabolic activities adapt to PD1 immune checkpoint blockade and how they associate with therapeutic benefits. To this end, we profiled metabolites in pre- and multiple on-treatment patient serum samples from three independent immunotherapy trials using hydrophilic interaction liquid chromatography coupled with either triple quadrupole MS multiple reaction monitoring or high resolution full scan MS detection. The study consisted of two Phase I trials (CA209-038, NCT01621490; CA209-009, NCT01358721) which included 78 patients with advanced melanoma and 91 patients with metastatic renal cell carcinoma (RCC) treated with nivolumab. To investigate the generalizability of our results, we also analyzed a large randomized Phase III trial (CheckMate 025, NCT01668784) with 743 RCC patients, among which 394 received nivolumab and 349 received everolimus. V600E is the most common BRAF mutation in melanoma and "BRAF_V600E" indicates the mutation status.
P falciparum asexual metabolomics following drug treatment (part-I)
STUDY_SUMMARY
P falciparum infected human red blood cells were treated with 10X IC50 drug for 2.5 hours, followed by extraction and analysis of polar metabolites using HPLC-MS or HPLC-MS/MS
INSTITUTE
Penn State
LAST_NAME
Llinas
FIRST_NAME
Manuel
ADDRESS
W126 Millennium Science Complex, University Park, PENNSYLVANIA, 16802, USA
Uropathogenic versus Urocolonizing Escherichia coli
STUDY_SUMMARY
Urinary tract infections (UTIs) represent a major burden across the population, although key facets of their pathogenesis challenge physicians and investigators alike. Escherichia coli epitomizes these obstacles: this Gram-negative bacterial species is the most prevalent agent of UTIs worldwide and can also colonize the urogenital tract in a phenomenon known as asymptomatic bacteriuria (ASB). Unfortunately, at the level of the organism, the relationship between symptomatic UTI and ASB is poorly defined, confounding our understanding of microbial pathogenesis and strategies for clinical management. Unlike diarrheagenic pathotypes of E. coli, the definition of uropathogenic E. coli (UPEC) remains phenomenologic, without conserved phenotypes and (known) genetic determinants that rigorously distinguish UTI- and ASB-associated strains. This manuscript provides a cross-disciplinary review of the current issues – from interrelated mechanistic and diagnostic perspectives – and describes new opportunities by which clinical resources can be leveraged to overcome molecular challenges. Specifically, we present our work harnessing a large collection of patient-derived isolates to identify features that do (and do not) distinguish UTI- from ASB-associated E. coli strains. Analyses of biofilm formation, previously reported to be higher in ASB strains, revealed extensive phenotypic heterogeneity that did not correlate with symptomatology. However, metabolomic experiments revealed distinct signatures between ASB and cystitis isolates, including species in the purine pathway (previously shown to be critical for intracellular survival during acute infection). Together, these studies demonstrate how large-scale, wild-type approaches can help dissect the physiology of colonization-versus-infection, suggesting that the molecular definition of UPEC may rest at the level of global bacterial metabolism.
INSTITUTE
Vanderbilt University
LAST_NAME
Rutledge
FIRST_NAME
Alexandra
ADDRESS
7330 Stevenson Center Lane, NASHVILLE, TENNESSEE, 37235, USA
Luteal lipids regulate progesterone production and may modulate immune cell function during the estrous cycle and pregnancy
STUDY_SUMMARY
Despite data indicating an important functional role for bioactive lipids in luteal function, little is known about the patterns of abundance of these lipids in corpus luteum (CL) during luteal development, maintenance, and rescue, in any species. Therefore, the abundance of lipid mediators, including endocannabinoids and oxylipins from cyclooxygenase (COX), lipoxygenase (LOX), and cytochrome P450 (CYP)-dependent metabolism were profiled in the CL on days 4, 11, and 18 of the estrous cycle and on day 18 of pregnancy. The objectives of this study were to identify lipid mediators that regulate luteal function during these transitions, to integrate the lipid profile with a previously published mRNA profile of CL during maternal recognition of pregnancy, and to determine the effect of a subset of lipids on in vitro progesterone production.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
TFPa/HADHA is required for fatty acid beta-oxidation and cardiolipin re-modeling in human cardiomyocytes (part-I)
STUDY_SUMMARY
Mitochondrial trifunctional protein deficiency, due to mutations in hydratase subunit A (HADHA), results in sudden infant death syndrome (SIDS) with no cure. To reveal the disease etiology, we generated stem cell-derived cardiomyocytes from HADHA-deficient hiPSCs and accelerated their maturation via a novel, engineered MicroRNA Maturation Cocktail (MiMaC) that upregulated the epigenetic regulator, HOPX. Fatty acid challenged MiMaC treated HADHA mutant cardiomyocytes manifested the disease phenotype: defective calcium dynamics and repolarization kinetics which resulted in a pro-arrhythmic state. Single cell RNA-seq revealed a novel cardiomyocyte developmental intermediate, based on metabolic gene expression. This intermediate gave rise to mature-like cardiomyocytes in control cells but, mutant cells transitioned to a pathological state with reduced fatty acid beta-oxidation (FAO), reduced mitochondrial proton gradient, disrupted cristae structure and defective cardiolipin remodeling. This study reveals that TFPa/HADHA, a MLCL-AT-like enzyme, is required for FAO and cardiolipin remodeling, essential for functional mitochondria in human cardiomyocytes.
INSTITUTE
UC Davis
LAST_NAME
Showalter
FIRST_NAME
Megan
ADDRESS
UC Davis Genome Center, room 1313, 451 Health Sci Drive
Longitudinal Characterization of the Fecal Metabolome in Dogs with Idiopathic Inflammatory Bowel Disease
STUDY_SUMMARY
Thirteen dogs diagnosed with idiopathic IBD, that previously failed to respond to treatment with elimination diets and metronidazole, were enrolled. Stool samples were collected from all dogs before initiating therapy with prednisone, after 3 and 8 weeks, and more than one year after beginning treatment. Thirteen healthy dogs were enrolled in the study as a control group.
The cecal and fecal metabolomes of horses before and after metronidazole administration
STUDY_SUMMARY
Metronidazole (15mg/kg BID PO) was given to horses (n=5) with in-dwelling cecal cannulas. The study was suspended after the fifth dose (day 3) due to adverse gastrointestinal effects. Cecal and fecal samples were obtained before and after (Days days -52, -28, -14, 0, 7, 14, 28 and 52) metronidazole administration. The metabolome was characterized by mass spectrometry-based methods. Fecal, but not cecal metabolites were affected by metronidazole. The fecal metabolites affected represented diverse metabolic pathways such as nucleic acid metabolism, secondary bile metabolism, fatty acid synthesis/degradation/elongation or metabolism and sugar metabolism.
Stool samples are acquired from mice models after biliary diversion surgery. Metabolite extractions are then performed on the stool samples and run through an optimized RPLC-IM-MS method.
The effects of a training program encompassing cold exposure, breathing exercises, and meditation on plasma metabomics during experimental human endotoxemia
STUDY_TYPE
Experimental human endotoxemia study
STUDY_SUMMARY
Study to investigate the effects of a training program encompassing cold exposure, breathing exercises, and meditation on plasma metabolomic during experimental human endotoxemia.
INSTITUTE
Radboud University Medical Centre Nijmegen
DEPARTMENT
Intensive Care Medicine
LABORATORY
Metabolomic Discoveries (acquired by Metabolon in September 2017)
LAST_NAME
Kox
FIRST_NAME
Matthijs
ADDRESS
Intensive Care Medicine (710), Geert Grooteplein 10
The sphingolipid, ceramide-1-phosphate (C1P), directly binds and activates Group IVA cytosolic phospholipase A2 (cPLA2) to generate eicosanoids. Due to the role of eicosanoids in wound healing, we choose to use our novel genetic mouse model expressing cPLA2 with an ablated C1P interaction site (KI) to examine the cPLA2/C1P interaction in wound healing. Wound closure rate was not affected, but wound maturation was enhanced by loss of the C1P/cPLA2α interaction based on the following findings. Wounds in KI mice displayed: i) increased infiltration of dermal fibroblasts into the wound environment; ii) increased wound tensile strength; and iii) higher Type I/Type III collagen ratios. These findings were recapitulated in vitro as primary dermal fibroblasts (pDFs) from KI mice showed significantly increased collagen deposition and migration velocity compared to WT and KO pDFs. Additionally, the KI showed an altered eicosanoid profile of reduced pro-inflammatory prostaglandins (PGE2) and increased levels of specific HETE species (5-HETE). Elevated 5-HETE levels promoted increased dermal fibroblast migration and collagen deposition. This “gain of function” role for the mutant cPLA2 was also linked to differential cellular localization of cPLA2α and 5-HETE biosynthetic factors. These studies demonstrate regulation of key biological mechanisms by a defined protein:lipid interaction in vivo and provide new insights into cPLA2 function.
Phenotyping Mouse blood metabolites in day and night in type 2 diabetes
STUDY_TYPE
time course in a 24hr period
STUDY_SUMMARY
This experiment compares the metabolites in control db/m and diabetic db/db in day and night.
INSTITUTE
Indiana University School of Medicine
DEPARTMENT
Ophthalmology
LABORATORY
Maria Grant Laboratory
LAST_NAME
Beli
FIRST_NAME
Eleni
ADDRESS
97 Lisburn Road
EMAIL
e.beli@qub.ac.uk
PHONE
5176144409
NUM_GROUPS
4
TOTAL_SUBJECTS
15
NUM_MALES
15
PUBLICATIONS
Nutrients.2019. Beli E. Loss of diurnal oscillatory rhythms in gut microbiota correlates with changes in circulating metabolites in type 2 diabetic, db/db mice
Eicosanoid profiles of dermal fibroblasts (part-II)
STUDY_SUMMARY
The sphingolipid, ceramide-1-phosphate (C1P), directly binds and activates Group IVA cytosolic phospholipase A2 (cPLA2) to generate eicosanoids. Due to the role of eicosanoids in wound healing, we choose to use our novel genetic mouse model expressing cPLA2 with an ablated C1P interaction site (KI) to examine the cPLA2/C1P interaction in wound healing. Wound closure rate was not affected, but wound maturation was enhanced by loss of the C1P/cPLA2α interaction based on the following findings. Wounds in KI mice displayed: i) increased infiltration of dermal fibroblasts into the wound environment; ii) increased wound tensile strength; and iii) higher Type I/Type III collagen ratios. These findings were recapitulated in vitro as primary dermal fibroblasts (pDFs) from KI mice showed significantly increased collagen deposition and migration velocity compared to WT and KO pDFs. Additionally, the KI showed an altered eicosanoid profile of reduced pro-inflammatory prostaglandins (PGE2) and increased levels of specific HETE species (5-HETE). Elevated 5-HETE levels promoted increased dermal fibroblast migration and collagen deposition. This “gain of function” role for the mutant cPLA2 was also linked to differential cellular localization of cPLA2α and 5-HETE biosynthetic factors. These studies demonstrate regulation of key biological mechanisms by a defined protein:lipid interaction in vivo and provide new insights into cPLA2 function.
Immunomodulatory activity of hyaluronidase is associated with metabolic adaptations during acute inflammation
STUDY_SUMMARY
Objective and design: Investigate survival outcomes, and immunological and metabolomic effects of hyaluronidase (Hz) treatment during mouse models of acute inflammation and sepsis. Methods: Survival of C57Bl/6 mice was monitored after lethal challenge with lipopolysaccharide (LPS) or cecal and ligation puncture (CLP)-induced sepsis and treated with Hz or saline. Mice were also challenged with LPS and treated with Hz for leukocyte counting, cytokine quantification and determination of metabolomic profiles in the peritoneal fluid. Results: Hz treatment improved survival outcomes after lethal challenge with LPS or CLPinduced sepsis. LPS challenge promoted acute neutrophil accumulation and production of interleukin-1β (IL-1β) and IL-6 in the peritoneum, whereas Hz treatment suppressed neutrophil infiltration and cytokine production. We further characterized the metabolomic alterations caused by LPS challenge, which predicted activity of metabolic pathways related to fatty acids and eicosanoids. Hz treatment had a profound effect over the metabolic response, reflected by reductions of the relative levels of fatty acids. Conclusion: Collectively, these data demonstrate that Hz treatment is associated with metabolic reprogramming of pathways that sustain the inflammatory response.
INSTITUTE
Sao Paulo University
DEPARTMENT
School of Pharmaceutical Sciences of Ribeirao Preto
Although health benefits of the Dietary Approaches to Stop Hypertension (DASH) diet are established, it is not understood which food compounds result in these benefits. We used a step-wise approach to identify unique compounds from individual foods of a DASH-style diet, determined if these Food-Specific Compounds (FSC) are detectable in urine, and then examined relationships between urinary FSC and blood pressure (BP). Nineteen subjects were randomized into 6-week controlled DASH-style diet interventions. Untargeted, LC/MS-based metabolomics was performed on 24-hour urine samples collected before and after each intervention and on 12 representative DASH-style foods.
Targeted Metabolomic Analysis in Patients with Wilson Disease Reveals Dysregulated Choline, Methionine and Aromatic Amino Acid Metabolism: Implications for Hepatic and Neurological Phenotypes
STUDY_TYPE
Cross-sectional
STUDY_SUMMARY
This study is comparing the plasma metabolomics profile of patients with the genetic disorder, Wilson disease, compared to healthy subjects matched by age, sex, and BMI. Wilson disease (WD) is a genetic copper overload condition characterized by hepatic and neuropsychiatric symptoms with a pathogenesis not well-understood. Choline is essential for lipid metabolism and the methionine cycle; a dysregulated methionine cycle is reported in animal models of WD, though not verified in humans. Defects in neurotransmitters, acetylcholine, and biogenic amines are reported in WD patients with neurological presentations. Precursors of these neuromodulators include choline, phenylalanine, tyrosine, and histidine. Less is known about the circulating levels of these precursors in WD. We aimed to study choline, methionine, aromatic amino acids, and phospholipids in serum profiles of WD subjects compared to healthy subjects (HC).
Metabolic changes of Fusobacterium nucleatum when co-cultured with other oral microbes (part-I)
STUDY_SUMMARY
We used membrane-separated co-culture systems to globally assess metabolomic changes of Fusobacterium nucleatum when co-cultured with Streptococcus gordonii and/or Veillonella parvula.
Metabolomic Profiling of Oxalate-Degrading Probiotic Lactobacillus acidophilus and Lactobacillus gasseri
STUDY_TYPE
Metabolomic/Lipidomic Profiling
STUDY_SUMMARY
Metabolomic and lipidomic profiling of Lactobacillus acidophilus and Lactobacillus gasseri to identify unique differences in their biochemistry that could potentially influence their ability to serve as probiotic agents for oxalate diseases.
INSTITUTE
University of Florida
DEPARTMENT
Pathology, Immunology and Laboratory Medicine
LABORATORY
Timothy J. Garrett, PhD
LAST_NAME
Chamberlain
FIRST_NAME
Casey
ADDRESS
UF Dept of Pathology PO Box 100275 Gainesville, FL 32610
Comparative metabolomics of MCF-7 breast cancer cells using different extraction solvents assessed by mass spectroscopy
STUDY_TYPE
Analysing metabolomics using GC Mass Spectroscopy
STUDY_SUMMARY
Metabolic profiling of cancer cells can play a vital role in revealing the molecular bases of cancer development and progression. In this study, gas chromatography coupled with mass spectrometry (GC-MS) was employed for the determination of signatures found in ER+/ PR+ breast cancer cells derived from MCF-7 using different extraction solvents including: A, formic acid in water; B, ammonium hydroxide in water; C, ethyl acetate; D, methanol: water (1:1, v/v); and E, acetonitrile: water (1:1, v/v). The greatest extraction rate and diversity of metabolites occurs with extraction solvents A and E. Extraction solvent D showed moderate extraction efficiency, whereas extraction solvent B and C showed inferior metabolite diversity. Metabolite set enrichment analysis results showed energy production pathways to be key in MCF-7 cell lines. This study showed that mass spectrometry could identify key metabolites associated with cancers. The highest enriched pathways were related to energy production as well as Warburg effect pathways, which may shed light on how energy metabolism has been hijacked to encourage tumour progression and eventually metastasis in breast cancer.
Metabolomic Profiles of Pancreatic β-Cells and Islets Exposed to Arsenic, part I β-Cells
STUDY_SUMMARY
Type-2 diabetes (T2D) is a complex metabolic disorder that affects hundreds of millions of people world-wide and is a growing public health concern. Despite recent advances in T2D research, the etiology of this disease and the mechanisms underlying the metabolic defects remain poorly understood. While obesity is thought to be the main cause for the rising prevalence of T2D, obesity alone cannot explain differences in the trends of T2D among different geographical regions and populations. Growing evidence suggests that environmental exposures to toxic and diabetogenic substances must play important roles. Inorganic arsenic (iAs) is a naturally occurring toxic metalloid. Hundreds of millions of people worldwide are exposed to unsafe levels of iAs in drinking water and food. iAs is a potent carcinogen, but iAs exposure has also been linked to increase risk of T2D. While the link between iAs exposure and T2D is well-established, the mechanisms underlying the diabetogenic effects of iAs exposure remain unclear. Results of our previously published and ongoing studies suggest that pancreatic β-cells are a primary target for iAs and its metabolites and that impaired insulin secretion by β-cells is the mechanism by which iAs exposure leads to diabetes. The proposed project will use metabolomics to identify metabolic pathways in β-cells that are targeted by iAs and its metabolites, monomethyl-As (MAs) and dimethyl-As (DMAs). The metabolomics data combined with results of our ongoing mechanistic studies will provide a comprehensive picture of the metabolic dysfunction leading to the development of diabetes in individuals exposed to iAs and of the molecular mechanisms that underlie this dysfunction. Identifying the affected pathways and mechanisms will ultimately help to improve strategies for prevention and/or treatment of T2D associated with chronic exposure to iAs.
Necrotizing soft-tissue infections (NSTIs) have multiple causes, risk factors, anatomical locations, and pathogenic mechanisms. In patients with NSTI, circulating metabolites may serve as substrate having impact on bacterial adaptation at the site of infection. Metabolic signatures associated with NSTI may reveal potential be useful as diagnostic and prognostic markers, as well as novel targets for therapy. This study used untargeted metabolomics analyses of plasma from NSTI patients (n=34) and healthy (non-infected) controls (n=24) to identify the metabolic signatures and connectivity patterns among metabolites associated with NSTI.
Colorectal cancer before and after surgery metabolomics data integration
STUDY_TYPE
Pilot study
STUDY_SUMMARY
In this study 40 urine samples were analyzed in 5 batches. There are 3 labels: control group volunteers (8 pcs., "CG"), colorectal cancer patients before surgical operation (20 pcs., "pre") and after surgical operation (12 pcs., "post").
Metabolomics-based profiling of the mode of action of Pathogen Box compounds in Trypanosoma brucei (part-I)
STUDY_SUMMARY
The mode of action of anti-Trypanosomal compounds from the Pathogen Box was investigated using an unbiased metabolomics approach. Trypanosoma brucei parasites were incubated for five hours with the test compounds at 0.5 µM concentration. Analysis of cell pellets allowed reproducible detection of diverse metabolites from a range of metabolic pathways.
INSTITUTE
Monash University
LAST_NAME
Creek
FIRST_NAME
Darren
ADDRESS
Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Melbourne, Victoria, 3052, Australia
Metabolomics-based profiling of the mode of action of Pathogen Box compounds in Trypanosoma brucei (part-II)
STUDY_SUMMARY
The mode of action of anti-Trypanosomal compounds from the Pathogen Box was investigated using an unbiased metabolomics approach. Trypanosoma brucei parasites were incubated for five hours with the test compounds at 0.5 µM concentration. Analysis of cell pellets allowed reproducible detection of diverse metabolites from a range of metabolic pathways.
INSTITUTE
Monash University
LAST_NAME
Creek
FIRST_NAME
Darren
ADDRESS
Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Melbourne, Victoria, 3052, Australia
Development and Characterisation of a Novel Class of Aroyl Guanidine Containing Anti-Trypanosomal Compounds
STUDY_SUMMARY
The mode of action of a novel class of aroyl guanidine containing anti-Trypanosomal compounds was investigated using an unbiased metabolomics approach. Trypanosoma brucei parasites were incubated for five hours with the test compounds at 1 µM concentration. Analysis of cell pellets allowed reproducible detection of diverse metabolites from a range of metabolic pathways.
INSTITUTE
Monash University
LAST_NAME
Creek
FIRST_NAME
Darren
ADDRESS
Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Melbourne, Victoria, 3052, Australia
Pseudoexfoliation Aqueous Humor Metabolites from Veterans Affairs Patients
STUDY_SUMMARY
We performed high-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) Isotopic Ratio Outlier Analysis of aqueous humor samples from patients from patients with pseudoefoliation syndrome (PEX).
POAG and Control Aqueous Humor IROA Metabolites from Veterans Affairs Patients
STUDY_TYPE
untargeted LC-MS/MS metabolomics IROA
STUDY_SUMMARY
We performed high-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis of the metabolome of POAG and Control patients. Samples were collected asynchronously.
Transgenic Parkinson's Mice Following Immunotherapy
STUDY_SUMMARY
An UHPLC-HRMS Metabolomics and Lipidomics Study of Stool from Transgenic Parkinson's disease Mice Following Immunotherapy. Parkinson’s disease (PD) is characterized by the loss of dopaminergic neurons in the substantia nigra pars compacta of the brain as well as degeneration of motor and non-motor circuitry. The cause of neuronal death is currently unknown, although chronic neuroinflammation, aggregated α-synuclein, mitochondrial dysfunction and oxidative stress have all been implicated. Gliosis has been shown to exacerbate neuroinflammation via secretion of pro-inflammatory cytokines, and there is a subsequent infiltration of T lymphocytes (T-cells), into the brain of PD patients. Using liquid chromatography-high resolution mass spectrometry (LC-HRMS), we have observed metabolomic changes in stool samples, thought to be associated with the potential disease-modifying effect of an immunotherapy administered to transgenic Parkinsonian (A53T) mice. Significant elevations (p<0.05) in metabolites associated with immune response (taurine, histamine and its methylated product, 3-methylhistamine) are identified as being higher in the mice undergoing immunotherapy. Furthermore, a reduction in triacylglycerols (TG) and diacylglyceols (DG) expression in stool following immunotherapy suggests a regulation of lipid breakdown or biosynthesis with the vaccine. These “omics” markers (among others reported in this article) along with weight gain and increased life expectancy suggest that the immunotherapy is positively modifying the disease state.
Lipid composition of isolated lipid droplets from the functional bovine corpus luteum
STUDY_TYPE
Lipidomics
STUDY_SUMMARY
Establishment and maintenance of pregnancy is dependent on progesterone synthesized by the corpus luteum (CL). The CL is known for the prominent presence of intracellular lipid droplets (LDs). However relatively little is known about the composition and function of these luteal LDs. Our objective was to identify the lipid composition of LDs from fully functional bovine CLs. Luteal LDs were isolated by flotation through a discontinuous sucrose gradient, lipids were then extracted using a standard Bligh and Dyer protocol, dried, and sent to Avanti Polar Lipids for lipidomics analysis. The samples were provided for lipidomic profiling of free sterols, cholesteryl esters, triglycerides, diacylglycerols, phospholipids, and sphingolipids. Molecular species were resolved by reversed-phase liquid chromatography in the presence of class and sub-class specific internal standard compounds added to each sample. The compounds were detected by tandem mass spectrometry (MS/MS) with scheduled multiple reaction monitoring (MRM) for mass-specific fragment ions according to the lipid class and molecular weight of the compound. Quantification of cholesterol, cholesteryl esters, triglycerides, and diglycerides were directly calculated with standards and internal standards from calibration response curves. The remaining lipid species were semi-quantization using the integrated area of each analyte’s MRM peak, divided by the appropriate internal standard peak area, and multiplied by the standard’s known concentration. Lipid concentrations were normalized to the corresponding protein concentration of each sample and as a mol % relative to total lipids or within each lipid class. Isolated luteal LDs were composed primarily of triglyceride (88%, mol% of lipid class to total lipids). Other neutral lipids included diacylglycerol, 2.9%; and cholesteryl esters, 1.5%. Polar lipids were primarily composed of phosphatidylcholine (3.1%), sphingomyelin (1.5%), phosphatidylinositol (0.9%), phosphatidylethanolamine (0.8%) and phosphatidylserine (0.4%). A number of other minor lipids representing less than 0.32% of the total lipid pool were also detected including phosphatidylglycerol, lysophospholipids, ceramides, and glycosylated ceramides. Lipid composition of bovine luteal LDs are distinct from LDs isolated from other tissues and in other species.
INSTITUTE
University of Nebraska Medical Center
DEPARTMENT
Obstetrics and Gynecology
LABORATORY
John S. Davis
LAST_NAME
Davis
FIRST_NAME
John
ADDRESS
983255 Nebraska Medical Center Omaha, NE 68198-3255
Luminal succinate in UC-HMA (human microbiota-associated) mice.
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Patients with ulcerative colitis (UC) are known to be at higher risk for Clostridium difficile (C. difficile) infection (CDI), and CDI in UC patients is recognized as a major clinical problem because it worsens UC outcome. In order to assess the role of gut dysbiosis, seen in UC patients, we have established a human microbiota-associated mouse model in which germ-free mice are colonized with gut microbiota from UC patients. Utilizing this model, we found that UC microbiota colonized HMA mice (UC-HMA mice) were susceptible to CDI. To address the mechanism by which UC-HMA mice are unable to acquire the colonization resistance against C. difficile, we analyzed the luminal metabolites in UC-HMA mice, especially in succinate which is a crucial metabolite doe the growth of C. difficile.
Lipidome Signatures of Metastasis in a Transgenic Mouse Model of Sonic Hedgehog Medulloblastoma.
STUDY_TYPE
Untargeted metabolomics
STUDY_SUMMARY
Metabolic alternations were investigated by applying Ultra Performance Liquid Chromatography Mass Spectrometry (UPLC-MS) to mice brain tissue samples collected from SmoA1-Math-GFP mice with (n=18) and without (n=7) metastasis. All samples were analyzed using reverse phase (RP) UPLC-MS analysis in positive and negative ion modes.
Determining secondary metabolite profile of Ilyonectria spp. pathogenic to ginseng root
STUDY_SUMMARY
This experiment aims to ascertain a profile of secondary metabolites produced by Ilyonectria species capable of causing disappearing root rot in ginseng. Ilyonectria isolates were grown on potato dextrose agar for 20 days, then plugs were taken from the cultures and extracted with ethyl acetate. Extracts were analyzed by LC-HRMS and tandem HRMS. Data were analyzed by Principal component analysis and molecular networking with GNPS.
Metabolomics and Hormonomics to Crack the Code of Filbert Growth
STUDY_SUMMARY
Introduction: Plants respond to changes in their environments through hormonal activation of a physiological cascade that redirects metabolic resources and growth. In filberts (Corylus sp.), chelated iron promotes the growth of new shoots but the mechanism(s) are not understood. Objectives: To use untargeted metabolomics and hormonomics approaches to generate novel hypotheses for the morphoregulatory role of ferric ethylenediamine-N,N'-di-(ortho-hydroxyphenyl) acetic acid (Fe-EDDHA) in filbert shoot organogenesis in vitro. Methods: Data were generated using previously optimized standardized untargeted metabolomics protocols with time of flight mass spectrometry. Multivariate statistical tools (principal component and partial least squares discriminant analysis) did not detect significant differences. Discovery tools Significance Analysis of Microarrays (SAM), multiple linear regression analysis, Bayesian analysis, logical algorithms, machine learning, synthetic biotransformations, targeted hormonomics, and online resources including MetaboAnalyst were used. Results: Starch/sucrose metabolism and shikimate pathway metabolites were increased. Dose dependent decreases were found in polyphenol metabolism, specifically ellagic acid and its methylated derivative 3,4,3'-tri-O-methylellagic acid. Hormonomics analysis revealed significant differences in phytohormones and their conjugates. FeEDDHA treatment reduced indole-3-acetic acid, abscisic acid, salicylic acid, jasmonic acid conjugates (JA-Trp, JA-Ile, OH-JA) and dihydrozeatinglucoside in regenerating explants. Serotonin (5HT) was decreased in FeEDDHA-treated regenerating tissues while the related metabolite melatonin was increased. Eight phenolic conjugates of 5HT and eight catabolites were affected by FeEDDHA indicating that metabolism to sequester, deactivate and metabolize 5HT was induced by Fe(III). Tryptophan was metabolized through kynurenine but not anthranilate. Conclusion: Seven novel hypotheses were generated to guide future studies to understand the regulatory control(s) of shoot organogenesis.
Metabolome Profiling of Synechococcus elongatus PCC 11801 strains engineered for Succinate Production
STUDY_TYPE
Measurement of relative metabolite pools of wild type and engineered Synechococcus elongatus PCC 11801 strains using Isotopic Ratio Method
STUDY_SUMMARY
Experiments to measure relative metabolite pools of wild type Synechococcus elongatus PCC 11801 and its recombinants producing succinate. The wild type and the engineered strains producing succinate were cultivated at 1% CO2 and their metabolome data was collected in three biological and three technical replicates (n=9). The study aims to find metabolomics changes between the wild type and the engineered to identify potential rate-limiting steps that be used as targets for improved production.
INSTITUTE
Indian Institute of Technology Bombay (IIT Bombay)
DEPARTMENT
Department of Chemical Engineering
LABORATORY
Bio systems Engineering Lab
LAST_NAME
Wangikar
FIRST_NAME
Pramod P
ADDRESS
Department of Chemical Engineering, IIT Bombay, Powai, Mumbai, Maharashtra, India - 400076
Metabolome Profiling of a Fast-growing Cyanobacterium Synechococcus elongatus PCC 11801 under Diurnal Cycle
STUDY_TYPE
Measurement of relative metabolite pools under diurnal cycle using isotopic ratio method
STUDY_SUMMARY
Experiments were carried out by growing Synechococcus elongatus PCC 11801 cells in multicultivators designed to provide sinusoidal light. The period was 14:10 (light-dark). The samples for metabolomics analysis were collected in the second diurnal cycle at an interval of 6 hours starting from 25th hour (25, 31, 37 and 43 hours). The light intensity amplitude was 600 µmole photons.m-2. s-1. Additionally samples were also collected using cells grown under continuous light illumination of 600 µmole photons.m-2. s-1 to compare the difference in metabolite levels compared to that in the diurnal cycle.
INSTITUTE
Indian Institute of Technology Bombay
DEPARTMENT
Department of Chemical Engineering
LABORATORY
Biosystems Engineering Lab
LAST_NAME
Wangikar
FIRST_NAME
Pramod P
ADDRESS
Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra, India - 400076
Transforming growth factor β (TGFβ) family comprises the main player in the development of fibrosis including three isoforms: TGFβ1, TGFβ2 and TGFβ3. TGFβ3 may play an antifibrotic role at the renal level, counteracting the role of TGFβ1, using a mouse model heterozygous for the TGFβ3 gene (TGFβ3+/-). Partial deletion of TGFβ3 causes in the mice albuminuria, loss of glomerular filtration rate, accelerated fibrosis, epithelial-to-mesenchymal transition and increment of glomerular basement membrane thickening.
Biomolecular analyses of hypospadias according to severity
STUDY_SUMMARY
Hypospadias, characterized by the displacement of the opening of the urethra at any point in the medial-ventral side of the penis, is classified upon severity as mild (Type I) and severe (Type II and Type III) hypospadias. Hypospadias’ etiology is idiopathic in the majority of cases, and underlying causes seem of multifactorial origin. Studies regarding genetic variants support this notion. It is unknown whether downstream gene products fit this profile. This study evaluated the metabolome of hypospadias by using the emerging technology of metabolomics in the search for distinct cellular processes associated with hypospadias’ etiology according to the severity of this congenital urogenital condition. Foreskin samples were collected during urethroplasty from boys with Type I, II, and III hypospadias or undergoing elective circumcision (N=28) between 5 to 28 months of age. Samples were processed and submitted to gas chromatography-mass spectrometry (GC/MS). MetaboloAnalyst (http://www.metaboanalyst.ca/) online platform was used for bioinformatic analyses. The metabolome of Type II and Type III hypospadias patients differs from the metabolome of Type I hypospadias and control patients. Thirty-five metabolites were identified by GC/MS. Of those, 14 metabolites, amino acids, were found in significantly low concentrations in Type II and Type III hypospadias in comparison to Type I hypospadias and controls. Amino acids comprised asparagine, aspartate, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, and tyrosine. The difference observed in the metabolome between severe and mild hypospadias supports previous research work of plausible severity-dependent etiologies for hypospadias. The observed downregulation of specific amino acids in severe hypospadias provides alternative routes for future research aiming to identify disrupted networks and pathways while considering the severity of hypospadias.
INSTITUTE
University of Puerto Rico, Medical Sciences Campus
DEPARTMENT
Anatomy & Neurobiology
LAST_NAME
Piñeyro-Ruiz
FIRST_NAME
Coriness
ADDRESS
University of Puerto Rico, Medical Sciences Campus, Department of Anatomy & Neurobiology, Main Building, 5th Floor, Room A-521 PO BOX 365067 San Juan, PR 00936-5067
Placental trophoblast cells are potentially at risk from circulating endocrine-disrupting chemicals, such as bisphenol A (BPA). To understand how BPA and the reputedly more inert bisphenol S (BPS) affect the placenta, C57BL6J mouse dams were fed 200 μg/kg body weight BPA or BPS daily for 2 wk and then bred. They continued to receive these chemicals until embryonic day 12.5, whereupon placental samples were collected and compared with unexposed controls. BPA and BPS altered the expression of an identical set of 13 genes. Both exposures led to a decrease in the area occupied by spongiotrophoblast relative to multinucleated giant cells (GCs) within the junctional zone, markedly reduced placental serotonin (5-HT) concentrations, and lowered 5-HT GC immunoreactivity. Concentrations of dopamine and 5-hydroxyindoleacetic acid, the main metabolite of serotonin, were increased. GC dopamine immunoreactivity was increased in BPA- and BPS-exposed placentas. A strong positive correlation between 5-HT+ GCs and reductions in spongiotrophoblast to GC area suggests that this neurotransmitter is essential for maintaining cells within the junctional zone. In contrast, an inverse correlation existed between dopamine+ GCs and reductions spongiotrophoblast to GC area. These outcomes lead to the following conclusions. First, BPS exposure causes almost identical placental effects as BPA. Second, a major target of BPA/BPS is either spongiotrophoblast or GC within the junctional zone. Third, imbalances in neurotransmitter-positive GC and an observed decrease in docosahexaenoic acid and estradiol, also occurring in response to BPA/BPS exposure, likely affect the placental–brain axis of the developing mouse fetus.
INSTITUTE
University of Missouri
DEPARTMENT
Life Sciences Center
LABORATORY
Univ. of Missouri Metabolomics Center
LAST_NAME
Sumner
FIRST_NAME
Lloyd
ADDRESS
1201 Rollins Street Columbia, Missouri 65211-7310
EMAIL
sumnerlw@missouri.edu
PHONE
573-882-5486
NUM_GROUPS
3 treatment X 2 sex = 6
TOTAL_SUBJECTS
40
PUBLICATIONS
Mao et al, Proceedings National Academy of Science, USA, 2020
Metabolomic Profiles of Pancreatic β-Cells and Islets Exposed to Arsenic, Islets (part-II)
STUDY_SUMMARY
Type-2 diabetes (T2D) is a complex metabolic disorder that affects hundreds of millions of people world-wide and is a growing public health concern. Despite recent advances in T2D research, the etiology of this disease and the mechanisms underlying the metabolic defects remain poorly understood. While obesity is thought to be the main cause for the rising prevalence of T2D, obesity alone cannot explain differences in the trends of T2D among different geographical regions and populations. Growing evidence suggests that environmental exposures to toxic and diabetogenic substances must play important roles. Inorganic arsenic (iAs) is a naturally occurring toxic metalloid. Hundreds of millions of people worldwide are exposed to unsafe levels of iAs in drinking water and food. iAs is a potent carcinogen, but iAs exposure has also been linked to increase risk of T2D. While the link between iAs exposure and T2D is well-established, the mechanisms underlying the diabetogenic effects of iAs exposure remain unclear. Results of our previously published and ongoing studies suggest that pancreatic islets are a primary target for iAs and its metabolites and that impaired insulin secretion by islets is the mechanism by which iAs exposure leads to diabetes. The proposed project will use metabolomics to identify metabolic pathways in β-cells that are targeted by iAs and its metabolites, monomethyl-As (MAs) and dimethyl-As (DMAs). The metabolomics data combined with results of our ongoing mechanistic studies will provide a comprehensive picture of the metabolic dysfunction leading to the development of diabetes in individuals exposed to iAs and of the molecular mechanisms that underlie this dysfunction. Identifying the affected pathways and mechanisms will ultimately help to improve strategies for prevention and/or treatment of T2D associated with chronic exposure to iAs.
Retargeting azithromycin-like compounds as antimalarials with dual modality
STUDY_SUMMARY
Resistance to front-line antimalarials (artemisinin combination therapies) is spreading, and development of new drug treatment strategies to rapidly kill Plasmodium parasites that cause malaria are urgently needed. Here, we show that azithromycin—a clinically used macrolide antibiotic that targets the bacterium-like ribosome of the malaria parasites apicoplast organelle and causes a slow-killing ‘delayed death’ phenotype—can also rapidly kill parasites throughout the asexual blood-stages of the lifecycle via a ‘quick-killing’ mechanism of action. Investigation of 84 azithromycin analogues revealed nanomolar quick-killing potency that is directed against the very earliest stage of parasite development within red blood cells. Indeed, the best analogue exhibited 1600-fold higher potency than azithromycin for in vitro treatment windows less than 48 hours. Analogues were also effective against the zoonotic malaria parasite P. knowlesi, and against both multi-drug and artemisinin resistant P. falciparum lines. Metabolomic profiles of azithromycin analogue treated parasites were similar to those of chloroquine treated parasites, suggesting that the quick-killing mechanism of action may in part be localised to the parasite food vacuole. However, metabolomic signatures associated with mitochondrial disruption were also present. In addition, unlike chloroquine, azithromycin and analogues were active across blood stage development, including merozoite invasion, suggesting that these macrolides have a multi-factorial mechanism of quick-killing activity. The positioning of functional groups added to azithromycin and its quick-killing analogues altered their activity against bacterial-like ribosomes but had minimal change on quick-killing activity, which suggests that apicoplast-targeting, delayed-death activity can either be preserved or removed independently of quick-killing. Apicoplast minus parasites remained susceptible to both azithromycin and its analogues, further demonstrating that quick-killing is independent of apicoplast-targeting, delayed-death activity. Therefore, development of azithromycin and analogues as antimalarials offers the possibility of targeting parasites through both a quick-killing and delayed death mechanism of action in a single, multifactorial chemotype.
INSTITUTE
Monash University
LAST_NAME
Siddiqui
FIRST_NAME
Ghizal
ADDRESS
381 Royal Parade, Parkville, Melbourne, Victoria, 3052, Australia
Time-course experiment of Microchloropsis gaditana cells supplemented with CO2
STUDY_TYPE
Time-course experiment
STUDY_SUMMARY
Experiments were conducted with Microchloropsis gaditana supplemented with very-low CO2 and high CO2. Sampling was done on the following time points: Day 3, 6 and 9.
INSTITUTE
International Centre for Genetic Engineering and Biotechnology
DEPARTMENT
Integrative Biology
LABORATORY
Omics of Algae
LAST_NAME
Jutur
FIRST_NAME
Pannaga Pavan
ADDRESS
2nd Floor, New Building, ICGEB, Aruna Asaf Ali Marg, New Delhi - 110067
EMAIL
jppavan@icgeb.res.in
PHONE
+91 11 26741358
STUDY_COMMENTS
Former name of species: Nannochloropsis gaditana Lubián
Maternal adiposity alters the human milk metabolome: a link between non-glucose monosaccharides and infant adiposity
STUDY_TYPE
untargeted metabolomics
STUDY_SUMMARY
An untargeted metabolomics analysis of human milk was performed to test the hypothesis that a unique human milk metabolome would emerge based on maternal adiposity (maternal fat mass and body mass index). This study also aimed to identify differentially expressed milk metabolites that are associated with fat mass in the infant. To our knowledge this study reports on the largest cohort to date examining the metabolomic differences in human milk composition between normal weight and obese women. Data generated from this study indicate the need for further research in the area of human milk metabolomics and the potential role for human milk small molecules in contributing to offspring growth and development.
INSTITUTE
University of California, Davis
DEPARTMENT
West Coast Metabolomics Center
LAST_NAME
Paglia
FIRST_NAME
Kelly
ADDRESS
451 Health Sciences Drive, Room 1313, Davis, CA, 95616, USA
Metabolomics Adaptation of Juvenile Pacific Abalone Haliotis discus hannai to Heat Stress
STUDY_SUMMARY
We compared two groups of abalones (from the same population) with different temperature acclimation history, through their survival at acute heat treatment and metabolites changes. The results indicated significantly higher survival for the high temperature acclimation group. Both groups experienced mitochondrial homeostasis break down during heat treatment, while the higher temperature acclimation group accumulated more metabolites beneficial to metabolic homeostasis, including various dipeptides, antioxidants, and neuroprotective substances.
INSTITUTE
Institute of Oceanology, Chinese Academy of Sciences
Untargeted lipidome changes in Chlamydomonas reinhardtii treated with small molecules containing adamantane structures
STUDY_SUMMARY
A study to investigate the effect of small molecule lipid inducing compounds that leads to hyper accumulation of lipids in N replete cells of Chlamydomonas reinhardtii. These compounds were identified through a high throughput screening designed for that purpose. During that screening, we screened 43,783 compounds and identified 367 primary hits. These 367 hits were further retested using a 8-point dilution series (from 0.25 to 30 uM) and verified the activity of 250 compounds that induce the hyper lipid accumulating phenotype in algae. Once the hit compounds were identified and confirmed, we then performed extensive chemoinformatics analysis to look for common scaffolds and identified several common substructures. We then selected 15 top performing compounds from 5 diverse structural groups and tested biochemical parameters such as growth, lipid accumulating capacity, effect on photosynthetic rates, respiration rates, oxygen consumption rates, analysis of different lipid species to quantify and identify fatty acid species using GC-MS. To understand the global changes in the lipidome, 2 structurally similar compounds were selected and compared with cells grown without compounds as control for untargeted lipidome analysis.
Multiplatform, non-targeted analysis of lung extracts of uninfected and Mtb-infected C57BL/6 mice at 4 and 9 weeks p.i.
STUDY_SUMMARY
The goal of this multiplatform, non-targeted metabolomics study was to explore the metabolic alterations occurring during the natural progression of pulmonary tuberculosis in a murine model of disease (C57BL/6 genotype). For this purpose, we used gas chromatography, capillary electrophoresis, and reversed-phase liquid chromatography coupled to high-resolution mass analyzers (GC-EI-QTOF/MS, CE-ESI(+)-QTOF/MS, LC-ESI(+)-QTOF/MS and LC-ESI(-)-QTOF/MS to analyze lung extracts of age and sex-matched uninfected mice (UW, n=4), Mycobacterium tuberculosis-infected mice at 4 weeks post-infection (4W, n=4) and Mycobacterium tuberculosis-infected mice at 9 weeks post-infection. All data were acquired in MS1 mode, following a canonical non-targeted workflow.
INSTITUTE
Universidad San Pablo-CEU, CEU Universities
DEPARTMENT
Departamento de Quimica y Bioquimica
LABORATORY
Centro de Metabolomica y Bioanalisis (CEMBIO)
LAST_NAME
Fernandez Garcia
FIRST_NAME
Miguel
ADDRESS
Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Spain
SS-31 and NMN: Two Paths to Improve Metabolism and Function in Aged Hearts
STUDY_SUMMARY
The effects of two different mitochondrial-targeted drugs, SS-31 and NMN, were tested on Old mouse hearts. After treatment with the drugs, individually or Combined, heart function was examined by echocardiography. SS-31 partially reversed an age-related decline in diastolic function while NMN fully reversed an age-related deficiency in systolic function at a higher workload. Metabolomic analysis revealed that both NMN and the Combined treatment increased nicotinamide and 1-methylnicotinamide levels, indicating greater NAD+ turnover, but only the Combined treatment resulted in significantly greater steady state NAD(H) levels. A novel magnetic resonance approach was used to assess how metabolite levels responded to changing workload. PCr/ATP decreased in response to increased workload in Old Control, but not Young, hearts, indicating an age-related decline in energetic capacity. Both drugs were able to normalize the PCr/ATP dynamics. SS-31 and NMN treatment also increased mitochondrial NAD(P)H production under the higher workload while only NMN increased NAD+ in response to the work jump. These measures did not shift in hearts given the Combined treatment, which may be owed to the enhanced NAD(H) levels in the resting state after this treatment. Overall, these results indicate that both drugs are effective at restoring different aspects of mitochondrial and heart health and that combining them results in a synergistic effect that rejuvenates Old hearts and best recapitulates the Young state.
Multi-omics of OsGF14b-mediated innate immunity against panicle blast in rice
STUDY_SUMMARY
In the present study, we used a multi-omics approach to decipher the molecular mechanisms of OsGF14b in governing panicle resistance to Magnaporthe oryzae.Results revealed OsGF14b mediated panicle blast resistance was involved in the activation of auxin and JA signaling pathways, resulting in reprogramming of the phenylpropanoid and diterpenoid pathway.
INSTITUTE
Agro-biological Gene Research Center , Guangdong Academy of Agricultural Sciences
Multi-omics of OsGF14b-mediated innate immunity against panicle blast in rice (part-II)
STUDY_SUMMARY
In the present study, we used a multi-omics approach to decipher the molecular mechanisms of OsGF14b in governing panicle resistance to Magnaporthe oryzae.Results revealed OsGF14b mediated panicle blast resistance was involved in the activation of auxin and JA signaling pathways, resulting in reprogramming of the phenylpropanoid and diterpenoid pathway.
INSTITUTE
Agro-biological Gene Research Center , Guangdong Academy of Agricultural Sciences
Huntington’s Disease Genotype Suppresses Global Manganese-Responsive Processes
STUDY_TYPE
Untargeted metabolomics analysis
STUDY_SUMMARY
Global untargeted metabolomics studies performed in the striatum tissue, the brain region most sensitive to neurodegeneration in Huntington’s Disease, to investigate global Mn-dependent and Mn-responsive biology following various Mn exposures in a mouse model of HD.
The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that responds to a variety of structurally diverse exogenous and endogenous small molecules. Gut microbiota utilizing tryptophan and indole metabolism as a reservoir, has been demonstrated to provide an abundant source of AHR ligands. So untargeted global profiling was performed to find the potential candidates of AHR activator in human feces.
INSTITUTE
The Pennsylvania State University
LAST_NAME
DONG
FIRST_NAME
FANGCONG
ADDRESS
314 Life Sciences Building, University Park, PA, 16802
The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that responds to a variety of structurally diverse exogenous and endogenous small molecules. Gut microbiota utilizing tryptophan and indole metabolism as a reservoir, has been demonstrated to provide an abundant source of AHR ligands. So differential analysis was performed to find the potential candidates of AHR activator in cecal contents between conventional and germ-free mice with the help of untargeted global profiling.
INSTITUTE
Pennsylvania State University
LAST_NAME
DONG
FIRST_NAME
FANGCONG
ADDRESS
314 Life Sciences Building, University Park, PA 16802
Disruption of Redox Balance Enhances the Effects of BRAF-inhibitors in Melanoma
STUDY_SUMMARY
Specifically, we report that drug-insensitive melanoma cells can maintain higher levels of antioxidant metabolites to withstand the lethal effects of drugs. By extending our analysis to other melanoma subtypes in the TCGA, we show that elevated redox capacity could indeed be a general feature of melanoma. Our results suggest that redox vulnerabilities could be exploited for therapeutic benefits and identify unsuspected combination targets to enhance the effects of BRAFi in pan-melanoma.
Metabolomic changes in mouse liver on a protein restricted diet
STUDY_SUMMARY
The data provided here are in support of the publication “Restriction of essential amino acids dictates the systemic metabolic response to dietary protein dilution” Yann W. Yap et al. Nature Communications 2020 (accepted for publication). Here we provide untargeted metabolomics LC-MS data from liver from C57Bl/6NCrl mice fed a diet in which dietary protein was restricted and corresponding unrestricted controls. Specifically, liver from animals on a low-protein diet following a week of diet adaptation and correspond controls with n = 5 for each group.
Metabolomic changes in mouse plasma on a protein restricted diet
STUDY_SUMMARY
The data provided here are in support of the publication “Restriction of essential amino acids dictates the systemic metabolic response to dietary protein dilution” Yann W. Yap et al. Nature Communications 2020 (accepted for publication). Here we provide untargeted metabolomics LC-MS data from plasma from C57Bl/6NCrl mice fed a diet in which dietary protein was restricted and corresponding unrestricted controls. Specifically, plasma from animals on a low-protein diet following a week of diet adaptation and correspond controls with n = 5 for each group.
Untargeted metabolomics in skeletal muscle of mice with chronic kidney disease
STUDY_TYPE
MS quantitative analysis
STUDY_SUMMARY
This study performed untargeted metabolomics analysis of skeletal muscle obtained form mice with and without chronic kidney disease.
INSTITUTE
University of Florida
LAST_NAME
Ryan
FIRST_NAME
Terence
ADDRESS
1864 Stadium Rd, FLG 114, Gainesville, FL, 32611, USA
EMAIL
ryant@ufl.edu
PHONE
352-294-1700
NUM_GROUPS
4
TOTAL_SUBJECTS
18
NUM_MALES
8
NUM_FEMALES
10
STUDY_COMMENTS
two control male samples processed mistakenly were from soles muscles, while all other samples were gastrocnemius muscles. Due to differences in fiber type proportions, soleus muscles were not used in final analysis
Exposure to paraben was associated with allergic outcomes, partially through the metabolomics changes. Urinary metabolomic analysis can be useful to elucidate the mechanisms underlying the associations between exposure to paraben and allergic outcomes.
INSTITUTE
Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital
Longitudinal wastewater sampling and untargeted metabolomics of three buildings
STUDY_SUMMARY
Direct sampling of building wastewater has the potential to enable "precision public health" observations and interventions. Temporal sampling offers additional dynamic information that can be used to increase the informational content of individual metabolic “features”, but few studies have focused on high-resolution sampling. Here, we sampled three spatially close buildings, revealing individual metabolomics features, retention time (rt) and mass-to-charge ratio (mz) pairs, that often possess similar stationary statistical properties, as expected from aggregate sampling. However, the temporal profiles of features—providing orthogonal information to physicochemical properties—illustrate that many possess different feature temporal dynamics (fTDs) across buildings, with large and unpredictable single day deviations from the mean. Internal to a building, numerous and seemingly unrelated features, with mz and rt differences up to hundreds of Daltons and seconds, display highly correlated fTDs, suggesting non-obvious feature relationships. Data-driven building classification achieves high sensitivity and specificity, and extracts building-identifying features found to possess unique dynamics. Analysis of fTDs from many short-duration samples allows for tailored community monitoring with applicability in public health studies.
Monophasic lipidomics extraction in cancer cell line
STUDY_TYPE
Lipidomics
STUDY_SUMMARY
We performed a comprehensive characterization of a monophasic extraction method in cancer cell lines. We used pharmacological perturbation on HepG2 cells to identify changes in different lipid families. We optimized the MS parameters, the chromatography and the data analysis to perform rapid and robust lipidomics analysis from cell lines.
Effect of BPA and genistein exposure on the fecal metabolome
STUDY_SUMMARY
Xenoestrogens are found in plant products, such as genistein (GEN), or industrial chemicals, such as bisphenol A (BPA), present in consumer products that are also pervasive in the environment. Early exposure to such endocrine disrupting chemicals (EDC) may affect neural development by inducing direct neural effects and/or through the microbiome-gut-brain axis. To test this hypothesis, California mice (Peromyscus californicus) offspring were exposed through the maternal diet to GEN (250 mg/kg feed weight) or BPA (5 mg/kg feed weight, low dose- LD and 50 mg/kg, upper dose-UD), and dams were placed on these diets two weeks prior to breeding, throughout gestation, and lactation. Various behaviors, gut microbiome, and fecal metabolome were assessed starting at 90 days of age. The LD but not UD of BPA resulted in individuals spending more time engaging in repetitive behaviors. GEN exposed individuals were more likely to exhibit such behaviors and showed socio-communicative disturbances. BPA and GEN exposed females had increased number of metabolites involved in carbohydrate metabolism and synthesis.. Males exposed to BPA or GEN showed alterations in lysine degradation and phenylalanine and tyrosine metabolism. Current findingsindicate cause for concern that developmental exposure to BPA or GEN might affect the microbiome-gut-brain axis.
INSTITUTE
University of Missouri
DEPARTMENT
MU Metabolomics Center
LAST_NAME
Sarma
FIRST_NAME
Saurav
ADDRESS
1201 Rollins street, 243 Bond Life Science Center, University of Missouri, Columbia, MO 65211, USA
Monophasic lipidomics extraction in cancer cell lines
STUDY_TYPE
Lipidomics
STUDY_SUMMARY
We performed a comprehensive characterization of a monophasic extraction method in cancer cell lines. We used pharmacological perturbation on HepG2 cells to identify changes in different lipid families. We optimized the MS parameters, the chromatography and the data analysis to perform rapid and robust lipidomics analysis from cell lines.
INSTITUTE
IGMM
LAST_NAME
Rodriguez Blanco
FIRST_NAME
Giovanny
ADDRESS
Crewe Road South, Edinburgh, Midlothian, EH42XU, United Kingdom
Core Functional Nodes and Sex-Specific Pathways in Human Ischemic and Dilated Cardiomyopathy
STUDY_SUMMARY
Restricted access to human left ventricular myocardium is a significant limitation in the study of heart failure (HF). Here, we utilise a large human heart biobank of carefully procured, cryopreserved left ventricular myocardium to obtain direct molecular insights into ischaemic (ICM) and dilated cardiomyopathy (DCM), the most common causes of HF worldwide1. We performed unbiased, deep proteomic and metabolomic analyses of 51 left ventricular (LV) samples from 44 cryopreserved human ICM and DCM hearts, including age-matched, histopathologically normal, donor controls of both genders for comparison. For the first time, we report perturbed thyroid hormone signalling pathways in the myocardium of both types of HF, and unveil the interaction of gender with HF, including increased nitric oxide-related arginine metabolism in male hearts, and many gender-specific mitochondrial and X chromosome-linked protein and metabolite changes. We provide all raw data, in addition to an interactive online application, as a publicly-available resource.
RP-UPLC-FTMS (+/- ion detection) were conducted on hippocampi from healthy (CON) and malnourished (MAL) mice, and MAL-BG (malnutrition plus E.coli/Bacteroidales exposure) mice.
INSTITUTE
University of British Columbia
DEPARTMENT
Microbiology and Immunology
LABORATORY
B. Brett Finlay
LAST_NAME
Bauer
FIRST_NAME
Kylynda
ADDRESS
Michael Smith Laboratories, #301 – 2185 East Mall, University of British Columbia Vancouver, British Columbia Canada, V6T 1Z4
Malnutrition and Liver Metabolomics Pre-Intervention (part-I)
STUDY_SUMMARY
RP-UPLC-FTMS (+/- ion detection) and HILIC-FTMS (+/- ion detection) were conducted on murine livers from healthy (CON) and malnourished (MAL) mice. To examine the impact of gut microbes and malnutrition, data was also collected from a third group (MBG).
INSTITUTE
University of British Columbia
DEPARTMENT
Microbiology and Immunology
LABORATORY
B. Brett Finlay
LAST_NAME
Bauer
FIRST_NAME
Kylynda
ADDRESS
Michael Smith Laboratories, #301 – 2185 East Mall, University of British Columbia Vancouver, British Columbia Canada, V6T 1Z4
Malnutrition and Liver Metabolomics Intervention (part-II)
STUDY_SUMMARY
RP-UPLC-FTMS (+/- ion detection) and HILIC-FTMS (+/- ion detection) were conducted on murine livers from healthy (CON) and malnourished model (MBG) mice. To examine the impact of dietary intervention the same untargeted metabolomics was conducted following an intervention treatment (CON, MBG, C-MBG, MBG-R groups). C-MBG = healthy to malnourished, MBG-R = malnourished model reversed on a healthy diet.
INSTITUTE
University of British Columbia
DEPARTMENT
Microbiology and Immunology
LABORATORY
B. Brett Finlay
LAST_NAME
Bauer
FIRST_NAME
Kylynda
ADDRESS
Michael Smith Laboratories, #301 – 2185 East Mall, University of British Columbia Vancouver, British Columbia Canada, V6T 1Z4
Grass pollen sublingual immunotherapy treatment induces transcriptomic and metabolic changes due to AIT treatment
STUDY_SUMMARY
47 patients were enrolled in a double-blind, placebo-controlled, multicenter trial using with GRAZAX® (Phleum pretense) during 2 years of therapy (T2). Immunological assays such as sIgE, sIgG4 and ISAC were carried out to the 31 patients who finished the trial. Additionally, serum and PBMCs samples from these samples were analyzed by metabolomics and transcriptomics, respectively. Based on their sensitization level, 22 patients were grouped in Mono and Poli groups, excluding epithelial allergic patients. Individuals were studied based on their treatment in Active and Placebo and their sensitization level. For metabolomics, samples were analyzed by Liquid and Gas Chromatography coupled to Mass Spectrometry (LC-MS and GC-MS, respectively).
INSTITUTE
Institute of Applied Molecular Medicine, CEU; The Centre of Metabolomics and Bioanalysis, CEU
LAST_NAME
Obeso Montero
FIRST_NAME
David
ADDRESS
Avda. Monteprincipe s/n 28668 Boadilla del Monte, Madrid, España
EMAIL
david.obesomontero@beca.ceu.es
PHONE
Tlf: 91 372 47 00 ext. 4662
NUM_GROUPS
2 main groups: Active and Placebo, and 2 subgroups: Monosensitized and Polisensitized patients.
Metabolomic profiling of Canadian species of Alternaria
STUDY_SUMMARY
This study aims to determine the predominant Alternaria species present in Canadian crops, their subsequent substrate distribution and which secondary metabolites are produced. 131 isolates obtained from the Canadian Collection of Fungal Cultures (CCFC) were grown as three-point inoculations on potato dextrose agar (PDA) and grown in the dark for seven days at 25°C. Each strain was extracted with ethyl acetate containing 1% formic acid, and analyzed by high resolution mass spectrometry (HRMS) in full MS mode in both positive and negative ionization modes at 140K resolution. Data were analyzed using principal component analysis (PCA), and groups were assigned based on k-means clustering analysis. All metabolites detected in the peak lists were investigated for significance (P<0.001) between groups using the Kruskal-Wallace test using Benjamini Hochberg false discovery rate (FDR) correction.
UPLC-MSE analysis of samples from Quercus ilex acorns flour. The objective of the study is to obtain a metabolomic profile of several acorns from different trees. This phytochemical analysis and characterization will be a base for the identification of bioactive, antinutritional, or toxic compounds and traceability analysis.
INSTITUTE
Universidad de Córdoba
DEPARTMENT
Department Biochemistry and Molecular Biology
LABORATORY
Agroforestry and Plant Biochemistry, Proteomics and Systems Biology
Targeting Sirt2 reprograms T cell metabolism for effective immune response
STUDY_TYPE
Targeted Metabolomics
STUDY_SUMMARY
There is a growing evidence that metabolism is a key driver of T cell functions. A switch from oxidative phosphorylation to aerobic glycolysis is a hallmark of T cell activation and is required to meet metabolic demands of proliferation and effector functions. However the mechanisms underlying the metabolic switch in T cells remain unclear. Here we identify Sirt2 as a crucial immune checkpoint coordinating metabolic and functional fitness of T cells. Sirt2 is induced upon T cells activation and increases in late maturation stages. Sirt2 negatively regulates glycolysis by targeting key glycolytic enzymes. Remarkably, Sirt2 knockout T cells exhibit profound upregulation of aerobic glycolysis with enhanced proliferation and effector function and thus effectively reject tumor challenge in vivo. Furthermore pharmacologic inhibition of Sirt2 in human tumor infiltrating lymphocytes demonstrated similar phenotype. Taken together our results demonstrate Sirt2 as an actionable target to reprogram T cell metabolism to augment immunotherapy.
Use of Information Dependent Acquisition mass spectra and Sequential Window Acquisition of all Theoretical fragment-ion mass spectra for fruit juices metabolomics and authentication
STUDY_SUMMARY
Introduction LC-MS based untargeted metabolomics are the main untargeted methods used for juice metabolomics to solve the authentication problem faced in fruit juice industry. Objectives To evaluate the performances of different untargeted metabolomics methods on fruit juices metabolomics and authentication, orange and apple fruit juices were selected for this study. Methods IDA-MS and SWATH-MS based on UHPLC-QTOF were used for the metabolomics and authenticity determination of apple and orange juices, including the lab-made samples of oranges (Citrus sinensis Osb.) from Jiangxi Province, apples (Malus domestica Borkh) from Shandong Province, and different brands of commercial orange and apple juice samples from markets. Results IDA-MS and SWATH-MS could both acquire numerous MS1 features and MS2 information of juice components, while SWATH-MS excels at the acquisition rate of MS2. Distinctive separation between authentic orange juice and not authentic orange juice could be seen from principal component analysis and hierarchical clustering analysis based on both IDA-MS and SWATH-MS. After analysis of variance, fold change analysis and orthogonal projection to latent structures discriminant mode, 53 and 46 potential markers were defined by IDA-MS and SWATH-MS (with 77.4% and 100% MS2 acquisition rate) separately. Subsequently, these potential markers were putatively annotated using general chemical databases with 6 more annotated by SWATH-MS. Furthermore, 7 of the potential markers, l-asparagine, umbelliferone, glucosamine, phlorin, epicatechin, phytosphingosine and chlorogenic acid, were identified with standards. For the consideration of model simplicity, two determined makers (umbelliferone and chlorogenic acid) were selected to construct the DD-SIMCA model in commercial samples because of their good correlation with apple adulteration proportion, and the sensitivity and specificity of the model were 100% and 95%. Conclusion SWATH-MS excels at the MS2 acquisition of juice components and potential markers. This study provides an overall performance comparison between IDA-MS and SWATH-MS, and guidance for the method selection on fruit juice metabolomics and juice authenticity determination. Two of the potential markers determined, umbelliferone and chlorogenic acid, could be used as apple juice indicators in orange juice.
INSTITUTE
China agricultural university
LAST_NAME
Xu
FIRST_NAME
Lei
ADDRESS
No. 17 Qinghua East Road, Haidian District, Beijing, Beijing, 100083, China
Fast and sensitive flow-injection mass spectrometry metabolomics by analyzing sample specific ion distributions
STUDY_SUMMARY
Mass spectrometry based metabolomics is a widely used approach in biotechnology and biomedical research. However, current methods coupling mass spectrometry with chromatography are time-consuming and not suitable for high-throughput analysis of thousands of samples. An alternative approach is flow-injection mass spectrometry (FI-MS) in which samples are directly injected to the ionization source. Here, we show that the sensitivity of Orbitrap FI-MS metabolomics methods is limited by ion competition effect in the detection system. We describe an approach for overcoming this effect by analyzing the distribution of ion m/z values and computationally determining a series of optimal scan ranges. This enables reproducible detection of ~9,000 and ~10,000 m/z features in metabolomics and lipidomics analysis of serum samples, respectively, with a sample scan time of ~15 seconds and duty time of ~30 seconds; a ~50% increase versus current spectral-stitching FI-MS. This approach facilitates high-throughput metabolomics for a variety of applications, including biomarker discovery and functional genomics screens.
Plasmodium falciparum increased time in circulation underlies persistent asymptomatic infection in the dry season
STUDY_SUMMARY
The dry season is a major challenge for Plasmodium falciparum parasites in many malaria endemic regions, where water availability limits mosquitoes to only part of the year. How P. falciparum bridges two transmission seasons months apart, without being cleared by the host or compromising host survival is poorly understood. Here we show that low levels of P. falciparum parasites persist in the blood of asymptomatic Malian individuals during the 5- to 6-month dry season, rarely causing symptoms and minimally affecting the host immune response. Parasites isolated during the dry season are transcriptionally distinct from those of subjects with febrile malaria in the transmission season, reflecting longer circulation within each replicative cycle, of parasitized erythrocytes without adhering to the vascular endothelium. Low parasite levels during the dry season are not due to impaired replication, but rather increased splenic clearance of longer-circulating infected erythrocytes. We propose that P. falciparum virulence in areas of seasonal malaria transmission is regulated so that the parasite decreases its endothelial binding capacity, allowing increased splenic clearance and enabling several months of subclinical parasite persistence.
INSTITUTE
Penn State
LAST_NAME
Llinas
FIRST_NAME
Manuel
ADDRESS
W126 Millennium Science Complex, University Park, PENNSYLVANIA, 16802, USA
Primary metabolites were quantified in human plasma from the 1:3 matched TEDDY case-control subjects. Information on the nested case-control study design can found in: Biomarker discovery study design for type 1 diabetes in The Environmental Determinants of Diabetes in the Young (TEDDY) study. Lee HS, Burkhardt B, McLeod W, Smith S, Eberhard C, Lynch K, Hadley D, Rewers M, Simell O, She JX, Hagopian W, Lernmark A, Akolkar B, Ziegler AG, Krischer J, and the TEDDY Study Group. Diabetes/Metabolism Research and Reviews. Epub 2013 December 15. doi: 10.1002/dmrr.2510 (PubMed ID: 24339168). Primary metabolites were extracted from 30 µl plasma aliquots by adding 1 ml of a carefully degassed -20 °C cold isopropanol/acetonitrile/water mixture (3:3:2, v/v/v) for 5 min at 4 °C which simultaneously precipitates proteins. After centrifugation, half of the extract was dried and cleaned up from triglycerides by a 50% acetonitrile mixture. After drying, internal standards were added as C08-C30 fatty acid methyl esters in chloroform as retention index markers (Kind et. al, 2009). Primary metabolites were derivatized by methoximation and trimethylsilylation. Primary metabolites were analyzed by cold injection/automatic liner exchange gas chromatography time-of- flight mass spectrometry (CIS/ALEX GC-TOF MS) (Fiehn et. al, 2008). In order to limit buildup of involatile material in the GC system and to prevent any carry over, an automatic liner exchange with multi-baffled liners and cold injection procedures was used instead of classic hot injections into standard s/sl liners. Multi-baffled inert glass liners were used because classic glass wool liners might hamper derivatization of amino groups for amino acid analysis. Robotic derivatization was further used to control reaction times (Ji et. al, 2011); and GC-columns were employed with integrated 10 meter guard columns, which could cut multiple times in 10 cm increments whenever quality control samples determined out-of-control situations. A temperature of 280 °C was determined to be the optimum transfer line temperature at which even higher-boiling compounds did not show tailing effects and at which the electron ionization filaments could still be operated at their optimal temperature of 250 °C and -70 eV. The mass spectrometer was operated using daily mass calibration auto-tuning using FC43 (perfluorotributyl-amine) and acquired 17 spectra per second and 1850-1950 V detector voltage. This high spectral acquisition rate was necessary to obtain enough data for mass spectral deconvolution of co-eluting compounds. Under these conditions, the system was around 10-times more sensitive than classic quadrupole GC-MS instruments and also clearly outperformed GC-triple quadrupole mass spectrometers. For select compounds, even lower limits of detection were achieved than for optimized MRM conditions in UPLC-QTRAP MS analysis. Around 144 unique metabolites were detectable in blood plasma (Fiehn & Kind, 2007); in addition to 221 unidentified compounds that were captured in the BinBase database system and hence, were comparable across studies. References: 1) Kind T, Wohlgemuth G, Lee DY, Lu Y, Palazoglu M, Shahbaz S, Fiehn O: FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry. Anal Chem 2009, 81(24):10038-10048. 2) Fiehn O, Wohlgemuth G, Scholz M, Kind T, Lee DY, Lu Y, Moon S, Nikolau B: Quality control for plant metabolomics: reporting MSI-compliant studies. Plant J 2008, 53(4):691-704. 3) Ji Y, Hebbring S, Zhu H, Jenkins GD, Biernacka J, Snyder K, Drews M, Fiehn O, Zeng Z, Schaid D et al: Glycine and a glycine dehydrogenase (GLDC) SNP as citalopram/escitalopram response biomarkers in depression: pharmacometabolomics-informed pharmacogenomics. Clin Pharmacol Ther 2011, 89(1):97-104. 4) Fiehn O, Kind T: Metabolite profiling in blood plasma. Methods Mol Biol 2007, 358:3-17. An explanation of the study design variables are explained in detail in a data dictionary provided in the raw data download section.
Metabolic Response in Patients with Post-Treatment Lyme Disease Symptoms/Syndrome
STUDY_SUMMARY
Post-treatment Lyme Disease Symptoms/Syndrome (PTLDS) occurs in approximately 10% of Lyme disease patients following antibiotic treatment. Objective biomarkers or specific clinical symptoms to identify PTLDS patients do not currently exist and the PTLDS classification is based on the report of persistent subjective symptoms for ≥ 6 months following antibiotic treatment for Lyme disease. Untargeted liquid chromatography-mass spectrometry metabolomics was used to define metabolic changes that occurred longitudinally in PTLDS and clinically cured non-PTLDS Lyme patients from two separate cohorts. An elastic net regularization model was applied to define the metabolites that classified PTLDS and non-PTLDS patients at different time points, and the PTLDS defining metabolites were evaluated in two sample cohorts using linear discriminant analysis. This study determined that observable metabolic alterations occur between PTLDS and non-PTLDS patients at multiple time points. These metabolic alterations discriminated between PTLDS and non-PTLDS patients and consisted of metabolites of glycerophospholipid, bile acid and acylcarnitine metabolism. Longitudinal analyses showed distinct patterns in metabolite abundance changes that indicated a greater variability in PTLDS vs non-PTLDS patients. These data provide evidence that an objective metabolite-based measurement can distinguish patients with PTLDS and help understand the underlying biochemistry of PTLDS.
INSTITUTE
Colorado State University
DEPARTMENT
MIP
LABORATORY
Belisle
LAST_NAME
Belisle
FIRST_NAME
John
ADDRESS
200 West Lake, Campus Delivery 0922, Colorado State University, Fort Collins, CO, 80523
Metabolomic study of Escherichia coli K-12 MG1655 and mutants
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
Metabolomic analysis of Wildtype, crp mutant and its five adaptively evolved populations evolved in glucose minimal media with 40 mM MOPS during its exponential phase of growth. Three biological and two technical replicate samples (n=6) were harvested for each of the strains while growing in a bioreactor aerobically at 37 degree Celsius and 700 rpm. This study aims to characterize and compare the metabolic profile of all these strains.
INSTITUTE
IIT Bombay
DEPARTMENT
Department of Chemical Engineering
LABORATORY
Systems Biology and Metabolic Engineering Laboratory
LAST_NAME
Pal
FIRST_NAME
Ankita
ADDRESS
IIT Bombay, Powai, Mumbai - 400076, Maharashtra, India
Time-course experiment of Microchloropsis gaditana cells supplemented with CO2 (part-II)
STUDY_TYPE
Time-course experiment
STUDY_SUMMARY
Experiments were conducted with Microchloropsis gaditana supplemented with very-low CO2 and high CO2. Sampling was done on the following time points: Day 3, 6 and 9.
INSTITUTE
International Centre for Genetic Engineering and Biotechnology
DEPARTMENT
Integrative Biology
LABORATORY
Omics of Algae
LAST_NAME
Jutur
FIRST_NAME
Pannaga Pavan
ADDRESS
2nd Floor, New Building, ICGEB, Aruna Asaf Ali Marg, New Delhi - 110067
EMAIL
jppavan@icgeb.res.in
PHONE
+91 11 26741358
STUDY_COMMENTS
Former name of species: Nannochloropsis gaditana Lubián
Quantitative Lipids study on total murine liver tissue from mice at different age
STUDY_TYPE
Liver tissue/Primary tissue
STUDY_SUMMARY
Following birth, the neonatal intestine is exposed to maternal and environmental bacteria that successively form a dense and highly dynamic intestinal microbiota. Whereas the effect of exogenous factors has been extensively investigated, endogenous, host-mediated mechanisms have remained largely unexplored. Concomitantly with microbial colonization, the liver undergoes functional transition from a hematopoietic organ to a central organ of metabolic regulation and immune surveillance. The aim of the present study was to analyze the influence of the developing hepatic function and liver metabolism on the early intestinal microbiota. Using metabolomic and microbial profiling in combination with multivariate analysis we characterized the colonization dynamics and liver metabolism in the murine gastrointestinal tract (n=6-10 per age group). We observed major age-dependent microbial and metabolic changes and identified bile acids as potent drivers of the early intestinal microbiota maturation. Consistently, oral administration of tauro-cholic acid or β-tauro-murocholic acid to newborn mice (n= 7-14 per group) accelerated postnatal microbiota maturation. Lipids in total liver tissue from healthy C57BL/6 mice at 1, 7, 14, 21, 28 and 56 day after birth was analyzed.
Quantitative Hexose study on total murine liver tissue from mice at different age
STUDY_TYPE
Liver tissue/Primary tissue
STUDY_SUMMARY
Following birth, the neonatal intestine is exposed to maternal and environmental bacteria that successively form a dense and highly dynamic intestinal microbiota. Whereas the effect of exogenous factors has been extensively investigated, endogenous, host-mediated mechanisms have remained largely unexplored. Concomitantly with microbial colonization, the liver undergoes functional transition from a hematopoietic organ to a central organ of metabolic regulation and immune surveillance. The aim of the present study was to analyze the influence of the developing hepatic function and liver metabolism on the early intestinal microbiota. Using metabolomic and microbial profiling in combination with multivariate analysis we characterized the colonization dynamics and liver metabolism in the murine gastrointestinal tract (n=6-10 per age group). We observed major age-dependent microbial and metabolic changes and identified bile acids as potent drivers of the early intestinal microbiota maturation. Consistently, oral administration of tauro-cholic acid or β-tauro-murocholic acid to newborn mice (n= 7-14 per group) accelerated postnatal microbiota maturation.Summed hexoses in total liver tissue from healthy C57BL/6 mice at 1, 7, 14, 21, 28 and 56 day after birth was analyzed.
Mechanism of Trichloroethylene (TCE) toxicity in the placenta
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Cells in culture will be exposed to S-(1,2-dichlorovinyl)-L-cysteine (DCVC), a relevant metabolite of TCE. The first cell line used will be HTR-8/SVneo, originally derived from first trimester female human cytotrophoblast cells and immortalized with simian virus 40 large T antigen, this cell line models first-trimester placental extravillous trophoblasts in vitro. HTR-8/SVneo cells will be cultured for 24 hours followed by exposure to cell culture media (control) or 20 µM DCVC for 6 or 12 hours. Cells (cells frozen in cell culture dish) will then be collected (n=5) In the TCE aim of this study, we will utilizeone cell model that phenotypically represents an important placental cell population.
Activation of ectopic olfactory receptor 544 induces GLP-1 secretion, alters gut microbiome, and improves intestinal permeability.
STUDY_TYPE
Fecal metabolome
STUDY_SUMMARY
Metabolome data set from mouse fecal samples Group - WT_AZA: fecal samples from wild type mouse fed with high fat diet and azelaic acid (0.05%, w/w) Group - WT_DW: fecal samples from wild type mouse fed with high fat diet Group - KO_AZA: fecal samples from Olfr544 receptor knock out mouse fed with high fat diet and azelaic acid (0.05%, w/w) Group - KO_DW: fecal samples from Olfr544 receptor knock out mouse fed with high fat diet
INSTITUTE
Korea University
LAST_NAME
Kim
FIRST_NAME
Jungyeon
ADDRESS
145, Anam-ro, Seongbuk-gu, Seoul, Seoul, 02841, Korea, South
Metabolomic profiling of baseline plasmas from a longitudinal prospective cohort of 491 active surveillance (AS) participants
STUDY_TYPE
Biomarker study
STUDY_SUMMARY
Untargeted metabolomics analyses were performed on clinically matched baseline plasma samples (n = 16 per group) prospectively collected from patients with clinically low-risk early stage prostate cancer undergoing AS who exhibited early disease progression (DP) (defined as upgrading of Gleason score (GS) and/or increased tumor volume on surveillance biopsy within 18 months after start of AS) or indolent disease (no progression for five or more years after start of AS) as well as 459 baseline plasma samples prospectively collected from patients with early-stage prostate cancer undergoing AS.
Plasma metabolites of lipid metabolism associate with diabetic polyneuropathy in a cohort with screen-tested type 2 diabetes: ADDITION-Denmark
STUDY_SUMMARY
The global rise in type 2 diabetes (T2D) is associated with a concomitant increase in diabetic complications. Diabetic polyneuropathy (DPN), the most frequent T2D complication, is characterized by sensory peripheral nerve damage. Although managing glucose effectively slows DPN progression in type 1 diabetes patients, it has limited efficacy in neuropathic T2D patients. The metabolic syndrome (MetS) recently emerged as a major risk factor for DPN; however, the metabolites associated with MetS that correlate with DPN are unknown. We conducted a global plasma metabolomics analysis from a cohort of patients enrolled in the Anglo-Danish-Dutch study of Intensive Treatment of Diabetes in Primary Care (ADDITION), including healthy control subjects, T2D patients, and T2D DPN patients. We identified 15 total plasma metabolites that were altered in T2D DPN patients, including lipids, amino acids, and energy-related metabolites. We evaluated the correlation between these metabolites and all lipid species to identify major changes in both plasma free fatty acids and complex lipids in T2D DPN patients, and found significant alterations in the abundance of long-chain saturated fatty acids, acylcarnitines, and sphingolipids. Our study suggests that DPN in T2D is associated with novel alterations in plasma metabolites related to lipid metabolism.
INSTITUTE
University of Michigan
LAST_NAME
Feldman
FIRST_NAME
Eva
ADDRESS
5017 AATBSRB, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200
Untargeted metabolomics analysis of in vitro headspace volatiles from 81 Pseudomonas aeruginosa bacterial isolates from individuals with cystic fibrosis. Headspace volatiles were collected using solid-phase microextraction (SPME) (in triplicate) and comprehensive two-dimensional gas chromatography and time-of-flight mass spectrometry (GCxGC-TOFMS). 15 replicates of un-inoculated media were prepared and analyzed in parallel, for a total of 258 samples.
Multi-omic profiling of primary mouse neutrophils reveals a pattern of sex and age-related functional regulation
STUDY_SUMMARY
Neutrophils are the most abundant white blood cells in humans and constitute one of the first lines of defense in the innate immune response. Neutrophils are extremely short-lived cells, which survive less than a day after reaching terminal differentiation. Thus, little is known about how organismal aging, rather than the daily cellular aging process, may impact neutrophil biology. In addition, accumulating evidence suggests that both immunity and organismal aging are extremely sex-dimorphic. Here, we describe a multi-omic resource of mouse primary bone marrow neutrophils from young and old female and male animals, at the transcriptomic, metabolomic and lipidomic levels. Importantly, we identify widespread age-related and sex-dimorphic regulation of ‘omics’ in neutrophils, specifically regulation of chromatin metabolism. We leverage machine-learning and identify candidate molecular drivers of age-related and sex-dimorphic transcriptional regulation of neutrophils. We leverage our resource to predict increased levels/release of neutrophil elastase in male mice. To date, this dataset represents the largest multi-omic resource for the study of neutrophils across biological sex and ages. This resource identifies molecular states linked to neutrophil characteristics linked to organismal age or sex, which could be leveraged to improve immune responses across individuals.
Metabolomic analysis of patients with recurrent angina
STUDY_TYPE
Case and control studies
STUDY_SUMMARY
This is a prospective study. After an overnight fast, venous blood was collected from patients with PCI. The patients were discharged after the blood draw. They were followed up every 30 days for angina recurrence up to 270 days (9 months). The samples were grouped into two groups: recurrent angina and angina-free based on the follow-up results at 9 months.
MYC regulates ribosome biogenesis and mitochondrial gene expression programs through its interaction with Host Cell Factor-1
STUDY_SUMMARY
MYC is an oncoprotein transcription factor that is overexpressed in the majority cancers. Although MYC itself is considered undruggable, it may be possible to inhibit MYC by targeting the co-factors it uses to drive oncogenic gene expression patterns. Here, we use loss- and gain- of function approaches to interrogate how one MYC co-factor—Host Cell Factor (HCF)-1—contributes to MYC activity in a Burkitt lymphoma setting. We identify high-confidence direct targets of the MYC–HCF-1 interaction that are regulated through a recruitment-independent mechanism, including genes that control mitochondrial function and rate-limiting steps for ribosome biogenesis and translation. We describe how these gene expression events impact cell growth and metabolism, and demonstrate that the MYC–HCF-1 interaction is essential for tumor maintenance in vivo. This work highlights the MYC–HCF-1 interaction as a focal point for development of novel anti-cancer therapies.
Transkingdom interactions between Lactobacilli and hepatic mitochondria attenuate western diet induced diabetes
STUDY_TYPE
Supplementation of mice with probiotic bacteria
STUDY_SUMMARY
For WD + Microbes 1 and WD + Microbes 3 experiments, C57BL/6 mice were fed western diet or western diet supplemented with Lactobacillus gasseri or Lactobacillus johnsonii for 8 weeks and serum was collected from each mice. For Pooled_1 (control group, western diet only), and Pooled_2 (western diet + Lactobacillus gasseri) groups, serum from 5 mice each was pooled. For Pooled_3 (western diet + Lactobacillus johnsonii) group, serum from 4 mice was pooled. For Pooled_7 (control group, western diet only), Pooled_8 (western diet + Lactobacillus gasseri) and Pooled_9 (western diet + Lactobacillus johnsonii) groups, serum from 6 mice each was pooled. For WD + Microbes 6 experiment, C57BL/6 mice were fed western diet for 8 weeks. Then, one group (n = 5) of mice was supplemented with Lactobacillus gasseri for 12 weeks along with continuation of western diet and serum was collected. For Pooled_10 (control group, western diet only) and Pooled_11 (western diet + Lactobacillus gasseri) groups, serum from 5 mice each was pooled. For GF + WD + LG experiment, C57BL/6 germ free mice were fed western diet or western diet supplemented with Lactobacillus gasseri for 2 weeks. For Pooled_12 (control, western diet only) and Pooled_13 (western diet + Lactobacillus gasseri) groups, serum from 2 mice each was pooled.
Sub-nanoliter metabolomics via mass spectrometry to characterize volume-limited samples
STUDY_SUMMARY
The human metabolome provides a window into the mechanisms and biomarkers of various diseases. However, because of limited availability, many sample types are still difficult to study by metabolomic analyses. Here, we present a new mass spectrometry (MS)-based metabolomics strategy that only consumes sub-nanoliter sample volumes. The approach consists of combining a customized metabolomics workflow with a pulsed MS ion generation method, known as triboelectric nanogenerator inductive nanoelectrospray ionization (TENGi nanoESI) MS. The first set of samples tested for this approach included exhaled breath condensates (EBC) collected from cystic fibrosis (CF) patients with impaired glucose tolerance to study the metabolome changes before and after the oral glucose tolerance test.
The human metabolome provides a window into the mechanisms and biomarkers of various diseases. However, because of limited availability, many sample types are still difficult to study by metabolomic analyses. Here, we present a new mass spectrometry (MS)-based metabolomics strategy that only consumes sub-nanoliter sample volumes. The approach consists of combining a customized metabolomics workflow with a pulsed MS ion generation method, known as triboelectric nanogenerator inductive nanoelectrospray ionization (TENGi nanoESI) MS. A second example to illustrate TENGi MS capabilities involves rare cell metabolomics of cultured mesenchymal stromal cells (MSCs), a cell type that has shown potential for treating a variety of chronic diseases. Examination of metabolic changes of MSCs cultured under conditions that may impact in vitro therapeutic activity, such as aggregate culture, or preconditioning with interferon gamma (IFN- γ)13, is critical for identifying attributes of cell quality. Reducing cell numbers required to perform MSC metabolomic analysis is essential for improving the manufacturing of highly therapeutic MSCs without significantly impeding production.
Metabolites in contents of small intestine in wild type and DAOG181R/G181R mice
STUDY_SUMMARY
To investigate if DAO regulates metabolites in intestinal lumen, we compared metabolites in contents of small intestine in wild type and DAOG181R/G181R mice. All mice have C57BL/6 background and 8 weeks of age.
The NIH sponsored multicenter Genetic Epidemiology of COPD (COPDGene (ClinicalTrials.gov Identifier: NCT01969344) study was approved and reviewed by the institutional review board at all participating centers (1). All study participants provided written informed consent. This study enrolled 10,198 non-Hispanic white (NHW) and African American (AA) individuals from January 2008 until April 2011 (Phase 1) who were aged 45-80 with ≥10 pack-year smoking history and no exacerbations for >30 days. In addition, 465 age and gender matched healthy individuals with no history of smoking were enrolled as controls (mostly at Phase 2). From July 2013 to July 2017, 5,697 subjects returned for an in-person 5-year visit. Each in-person visit included spirometry before and after albuterol, quantitative CT imaging of the chest, and blood sampling. From two clinical centers (National Jewish Health and University of Iowa) 162 subjects at Phase 1 (all NHW) and 1,136 subjects (1,040 NHW, 96 AA) participated in an ancillary study in which they provided fresh frozen plasma collected using an 8.5 ml p100 tube (Becton Dickinson) at Phase 2.
Five Easy Metrics of Data Quality for LC-MS based Global Metabolomics
STUDY_SUMMARY
Data quality in global metabolomics is of great importance for biomarker discovery and systems biology studies. However, comprehensive metrics and methods to evaluate and compare the data quality of global metabolomics data sets are lacking. In this work, we combine newly developed metrics, along with well-known measures, to comprehensively and quantitatively characterize the data quality across two similar LC-MS platforms, with the goal of providing an efficient and improved ability to evaluate the data quality in global metabolite profiling experiments. A pooled human serum sample was run 50 times on two high-resolution LC-QTOF-MS platforms to provide profile and centroid MS data. These data were processed using Progenesis Qi software and then analyzed using five important data quality measures, including retention time drift, compound coverage, missing values and MS reproducibility (2 measures). The coverage was fit to a Gamma distribution versus compound abundance, which was normalized to allow comparison of different platforms. To evaluate missing values, characteristic curves were obtained by plotting the compound detection percentage versus extraction frequency. To characterize reproducibility, the accumulative coefficient of variation (CV) versus percentage of total compounds detected and CV vs intra-class correlation coefficient (ICC) were investigated. Key findings include significantly better performance using profile mode data compared to centroid mode as well quantitatively better performance from the newer, higher resolution instrument. A summary of the results given in tabulated form gives a snapshot of the experimental results and provides a template to evaluate the global metabolite profiling workflow. In total, these measures give a good overall view of data quality in global profiling and allow comparisons of data acquisition strategies and platforms as well as optimization of parameters.
INSTITUTE
University of Washington
DEPARTMENT
Anesthesiology and Pain
LABORATORY
Daniel Raftery
LAST_NAME
Zhang
FIRST_NAME
Xinyu
ADDRESS
850 Republican Street, Seattle, Washington 98109, United States
Targeted metabolomic analysis on hexosamine biosynthetic pathway in flies on time restricted feeding
STUDY_TYPE
metabolomic identification
STUDY_SUMMARY
The integration of circadian and metabolic signals is essential for maintaining robust circadian rhythms and ensuring efficient metabolism and energy use. Using Drosophila as an animal model, we showed observed strong correlation between daily daily rhythms of protein O-linked N-acetylglucosaminylation (O-GlcNAcylation) and clock-controlled feeding-fasting cycles, suggesting that O-GlcNAcylation rhythms are primarily driven by nutrient input. Interestingly, daily O-GlcNAcylation rhythms were severely dampened when we subjected flies to time-restricted feeding (TRF) at unnatural feeding time. This suggests the presence of a clock-regulated buffering mechanism that prevents excessive O-GlcNAcylation at non-optimal times of the day-night cycle, which could disrupt circadian health. We performed targeted metabolomic analysis on hexosamine biosynthetic pathway (HBP), which produces UDP-GlcNAc (the substrate for O-GlcNAcylation), to evaluate the daily activity of HBP enzymes under TRF conditions. We found glutamine--fructose-6-phosphate amidotransferase (GFAT) mediates this buffering mechanism.
Metabolomics of lung injury after allogeneic hematopoietic cell transplantation - Liver ICMS
STUDY_TYPE
preliminary data
STUDY_SUMMARY
Allogeneic hematopoietic cell transplantation (allo-HCT) is a potentially curative treatment option for a variety of hematological malignancies. Interactions between the donor immune system and the patient tissue result in a disease, called GVHD. The pathophysiology of acute GVHD can be hypothesized in three sequential phases: cytokine storm and activation of the antigen-presenting cells (APC), donor T cell activation and effector cell phase. Idiopathic pneumonia syndrome (IPS) is one of the most deleterious complications after allogeneic HCT and is considered not only to be related to conditioning regimen toxicity but also represents an end organ damage caused by allo-reactive T cells, therefore making the lung susceptible to a two-pronged attack, one of which overlaps with GVHD causing other target organ injury. IPS results in mortality of up to 90% of patients. We will use a murine model of IPS and GVHD which is well established in our group, and in which disease evolves either across disparities in major histocompatibility complex (MCH) class I and II, minor histocompatibility antigens (miHags) or both. Metabolomics changes following syngeneic and allogeneic HCT at post-transplantation Days +7 (cytokine storm phase) and Days +42 (cellular effector phase) are compared to baseline wild-type (naive) controls. Prior to analysis, naïve - and experimental mice (N=3 from each group) were fed with semi-liquid diet supplemented with tracers (13C6-glucose ) over 24 hours. At the end of 7 days or 42 days, respectively, feces and aGVHD target organs (colon, liver and lung) were collected from all groups and further processed and / or analyzed. We expect to reveal metabolic pathways affected after allo-HCT which contribute to immune cell mediated lung injury (IPS) and will potentially identify different metabolic pathways in other GVHD target organs.
INSTITUTE
University of Kentucky
DEPARTMENT
MCC
LAST_NAME
Hildebrandt
FIRST_NAME
Gerhard
ADDRESS
CTW-453, 900 South Limestone street. UKY. Lexington, Kentucky-40536
Global metabolomics of IFNy cued neurogenic NSCs seeded on hydrogel
STUDY_SUMMARY
Neural stem cells (NSCs) provide a strategy to replace damaged neurons following traumatic central nervous system injuries. A major hurdle to translation of this therapy is that direct application of NSCs to CNS injury does not support sufficient neurogenesis due to lack of proper cues. To provide prolonged spatial cues to NSCs IFN-γ was immobilized to biomimetic hydrogel substrate to supply physical and biochemical signals to instruct the encapsulated NSCs to be neurogenic. However, the immobilization of factors, including IFN-γ, versus soluble delivery of the same factor, has been incompletely characterized especially with respect to activation of signaling and metabolism in cells over longer time points. In this study, protein and metabolite changes in NSCs induced by immobilized versus soluble IFN-γ at 7 days were evaluated. Soluble IFN-γ, refreshed daily over 7 days, elicited stronger responses in NSCs compared to immobilized IFN-γ indicating that immobilization may not sustain signaling or has altered ligand/receptor interaction and integrity. However, both IFN-γ delivery types supported increased βIII tubulin expression in parallel with canonical and non-canonical receptor-signaling compared to no IFN-γ. Global metabolomics and pathway analysis revealed that soluble and immobilized IFN-γ altered metabolic pathway activities including energy, lipid and amino acid synthesis, with soluble IFN-γ having the greatest metabolic impact overall.
INSTITUTE
University of Akron
DEPARTMENT
Chemistry
LABORATORY
Shriver lab
LAST_NAME
Baumann
FIRST_NAME
Hannah
ADDRESS
190 E. Buchtel Common
EMAIL
hjb17@zips.uakron.edu
PHONE
4198864033
NUM_GROUPS
3
PUBLICATIONS
Metabolomic and Signaling Programs Induced by Immobilized versus Soluble IFN γ in Neural Stem Cells
Dynamic binning peak detection and assessment of various lipidomics liquid chromatography-mass spectrometry pre-processing platforms
STUDY_SUMMARY
Liquid chromatography-mass spectrometry (LC-MS) based lipidomics generate a large dataset, which requires high-performance data pre-processing tools for their interpretation such as XCMS, mzMine and Progenesis. These pre-processing tools rely heavily on accurate peak detection, which depends on setting the peak detection mass tolerance (PDMT) properly. The PDMT is usually set with a fixed value in either ppm or Da units. However, this fixed value may result in duplicates or missed peak detection. Therefore, we developed the dynamic binning method for accurate peak detection, which takes into account the peak broadening described by well-known physics laws of ion separation and set dynamically the value of PDMT as a function of m/z. Namely, in our method, the PDMT is proportional to for FTICR, to for Orbitrap, to m/z for Q-TOF and is a constant for Quadrupole mass analyzer, respectively. The dynamic binning method was implemented in XCMS. Our further goal was to compare the performance of different lipidomics pre-processing tools to find differential compounds. We have generated set samples with 43 lipids internal standards differentially spiked to aliquots of one human plasma lipid sample using Orbitrap LC-MS/MS. The performance of the various pipelines using aligned parameter sets was quantified by a quality score system which reflects the ability of a pre-processing pipeline to detect differential peaks spiked at various concentration levels. The quality score indicates that the dynamic binning method improves the performance of XCMS (maximum p-value 9.8·10-3 of two-sample Wilcoxon test). The modified XCMS software was further compared with mzMine and Progenesis. The results showed that modified XCMS and Progenesis had a similarly good performance in the aspect of finding differential compounds. In addition, Progenesis shows lower variability as indicated by lower CVs, followed by XCMS and mzMine. The lower variability of Progenesis improve the quantification, however, provide an incorrect quantification abundance order of spiked-in internal standards.
INSTITUTE
University of Groningen, Netherlands
LAST_NAME
Péter
FIRST_NAME
Horvatovich
ADDRESS
Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
EMAIL
p.l.horvatovich@rug.nl
PHONE
+31 (0)50 363 3341
NUM_GROUPS
6
TOTAL_SUBJECTS
1
STUDY_COMMENTS
Different concentrations of lipid standard mixture were added to the plasma lipid extract aliquots
Metabolomics of murine embryos cultured in a microfluidic device and comparison with traditional microdrops culture
STUDY_SUMMARY
Global untargeted metabolomics study to analyse culture media extracted from an innovative microfluidic device or traditional microdrops in presence or absence of murine embryos to investigate PDMS-release of biomolecules and embryo metabolic activity.
To apply this method in a pilot study, we spiked either taurine or sulfoquinovose into an in vitro simplified human microbiota model with and without Bilophila wadsworthia, a known sulfonate utilizer.
Metabolomics reveals the protective effect of isosteviol sodium against multiple organ injury in septic mice - Sample Type: Heart, Ion Mode: Pos/Neg (part- Heart_ Pos/Neg)
STUDY_SUMMARY
Sepsis is a severe inflammatory disorder that can lead to multiple organ injury. Isosteviol sodium (STV-Na) is a terpenoid derived from stevioside that exerts anti-inflammatory, antioxidant and anticancer activities. However, the influence of STV-Na on sepsis remains unknown. Here, we assessed the potential effects of STV-Na on sepsis and multiple organ injury induced by lipopolysaccharide (LPS). We found that STV-Na increased the survival rate of mice treat with LPS, significantly improved the functions of the heart, lung, liver, and kidney, and reduced the production of inflammatory cytokines. Moreover, Multiorgan metabolomics analysis demonstrated that glutathione metabolism, purine metabolism, glycerophospholipid metabolism and pantothenate and CoA biosynthesis, were significantly altered by STV-Na. This study provides novel insights into the metabolite changes of multiple organ injury in septic mice, which may help characterize the underlying mechanism and provide an improved understanding of the therapeutic effects of STV-Na on sepsis. Mice are randomly assigned to 4 groups in study design. Control: saline + saline Model: saline + LPS; Treatment: STV-Na + LPS; Positive: dexamethasone (Dex) + LPS. Drugs were administered i.p. Six hours after LPS injection, mice were sacrificed. And blood and tissues (heart, lung, liver, spleen and kidney) were subjected to UHPLC-TIMS TOF MS/MS-based metabolomics analyses.
INSTITUTE
Guangdong University of Technology
LAST_NAME
Wang
FIRST_NAME
Shanping
ADDRESS
No. 100, Waihuan Xilu, Guangzhou Higher Education Mega Center, Panyu District,
Metabolomics reveals the protective effect of isosteviol sodium against multiple organ injury in septic mice - Liver
STUDY_SUMMARY
Sepsis is a severe inflammatory disorder that can lead to multiple organ injury. Isosteviol sodium (STV-Na) is a terpenoid derived from stevioside that exerts anti-inflammatory, antioxidant and anticancer activities. However, the influence of STV-Na on sepsis remains unknown. Here, we assessed the potential effects of STV-Na on sepsis and multiple organ injury induced by lipopolysaccharide (LPS). We found that STV-Na increased the survival rate of mice treat with LPS, significantly improved the functions of the heart, lung, liver, and kidney, and reduced the production of inflammatory cytokines. Moreover, Multiorgan metabolomics analysis demonstrated that glutathione metabolism, purine metabolism, glycerophospholipid metabolism and pantothenate and CoA biosynthesis, were significantly altered by STV-Na. This study provides novel insights into the metabolite changes of multiple organ injury in septic mice, which may help characterize the underlying mechanism and provide an improved understanding of the therapeutic effects of STV-Na on sepsis.
INSTITUTE
Guangdong University of Technology
LAST_NAME
Wang
FIRST_NAME
Shanping
ADDRESS
No. 100, Waihuan Xilu, Guangzhou Higher Education Mega Center, Panyu District,
Metabolomics reveals the protective effect of isosteviol sodium against multiple organ injury in septic mice - Lung
STUDY_SUMMARY
Sepsis is a severe inflammatory disorder that can lead to multiple organ injury. Isosteviol sodium (STV-Na) is a terpenoid derived from stevioside that exerts anti-inflammatory, antioxidant and anticancer activities. However, the influence of STV-Na on sepsis remains unknown. Here, we assessed the potential effects of STV-Na on sepsis and multiple organ injury induced by lipopolysaccharide (LPS). We found that STV-Na increased the survival rate of mice treat with LPS, significantly improved the functions of the heart, lung, liver, and kidney, and reduced the production of inflammatory cytokines. Moreover, Multiorgan metabolomics analysis demonstrated that glutathione metabolism, purine metabolism, glycerophospholipid metabolism and pantothenate and CoA biosynthesis, were significantly altered by STV-Na. This study provides novel insights into the metabolite changes of multiple organ injury in septic mice, which may help characterize the underlying mechanism and provide an improved understanding of the therapeutic effects of STV-Na on sepsis.Mice are randomly assigned to 4 groups in study design. Control: saline + saline Model: saline + LPS; Treatment: STV-Na + LPS; Positive: dexamethasone (Dex) + LPS. Drugs were administered i.p. Six hours after LPS injection, mice were sacrificed. And blood and tissues (heart, lung, liver, spleen and kidney) were subjected to UHPLC-TIMS TOF MS/MS-based metabolomics analyses.
INSTITUTE
Guangdong University of Technology
LAST_NAME
Wang
FIRST_NAME
Shanping
ADDRESS
No. 100, Waihuan Xilu, Guangzhou Higher Education Mega Center, Panyu District,
Metabolomics reveals the protective effect of isosteviol sodium against multiple organ injury in septic mice - Kidney
STUDY_SUMMARY
Sepsis is a severe inflammatory disorder that can lead to multiple organ injury. Isosteviol sodium (STV-Na) is a terpenoid derived from stevioside that exerts anti-inflammatory, antioxidant and anticancer activities. However, the influence of STV-Na on sepsis remains unknown. Here, we assessed the potential effects of STV-Na on sepsis and multiple organ injury induced by lipopolysaccharide (LPS). We found that STV-Na increased the survival rate of mice treat with LPS, significantly improved the functions of the heart, lung, liver, and kidney, and reduced the production of inflammatory cytokines. Moreover, Multiorgan metabolomics analysis demonstrated that glutathione metabolism, purine metabolism, glycerophospholipid metabolism and pantothenate and CoA biosynthesis, were significantly altered by STV-Na. This study provides novel insights into the metabolite changes of multiple organ injury in septic mice, which may help characterize the underlying mechanism and provide an improved understanding of the therapeutic effects of STV-Na on sepsis.
INSTITUTE
Guangdong University of Technology
LAST_NAME
Wang
FIRST_NAME
Shanping
ADDRESS
No. 100, Waihuan Xilu, Guangzhou Higher Education Mega Center, Panyu District,
Metabolomics reveals the protective effect of isosteviol sodium against multiple organ injury in septic mice - Spleen
STUDY_SUMMARY
Sepsis is a severe inflammatory disorder that can lead to multiple organ injury. Isosteviol sodium (STV-Na) is a terpenoid derived from stevioside that exerts anti-inflammatory, antioxidant and anticancer activities. However, the influence of STV-Na on sepsis remains unknown. Here, we assessed the potential effects of STV-Na on sepsis and multiple organ injury induced by lipopolysaccharide (LPS). We found that STV-Na increased the survival rate of mice treat with LPS, significantly improved the functions of the heart, lung, liver, and kidney, and reduced the production of inflammatory cytokines. Moreover, Multiorgan metabolomics analysis demonstrated that glutathione metabolism, purine metabolism, glycerophospholipid metabolism and pantothenate and CoA biosynthesis, were significantly altered by STV-Na. This study provides novel insights into the metabolite changes of multiple organ injury in septic mice, which may help characterize the underlying mechanism and provide an improved understanding of the therapeutic effects of STV-Na on sepsis.
INSTITUTE
Guangdong University of Technology
LAST_NAME
Wang
FIRST_NAME
Shanping
ADDRESS
No. 100, Waihuan Xilu, Guangzhou Higher Education Mega Center, Panyu District,
Metabolomics reveals the protective effect of isosteviol sodium against multiple organ injury in septic mice - Plasma
STUDY_SUMMARY
Sepsis is a severe inflammatory disorder that can lead to multiple organ injury. Isosteviol sodium (STV-Na) is a terpenoid derived from stevioside that exerts anti-inflammatory, antioxidant and anticancer activities. However, the influence of STV-Na on sepsis remains unknown. Here, we assessed the potential effects of STV-Na on sepsis and multiple organ injury induced by lipopolysaccharide (LPS). We found that STV-Na increased the survival rate of mice treat with LPS, significantly improved the functions of the heart, lung, liver, and kidney, and reduced the production of inflammatory cytokines. Moreover, Multiorgan metabolomics analysis demonstrated that glutathione metabolism, purine metabolism, glycerophospholipid metabolism and pantothenate and CoA biosynthesis, were significantly altered by STV-Na. This study provides novel insights into the metabolite changes of multiple organ injury in septic mice, which may help characterize the underlying mechanism and provide an improved understanding of the therapeutic effects of STV-Na on sepsis.
INSTITUTE
Guangdong University of Technology
LAST_NAME
Wang
FIRST_NAME
Shanping
ADDRESS
No. 100, Waihuan Xilu, Guangzhou Higher Education Mega Center, Panyu District,
A Metabolomic Signature of Glucagon Action in Healthy Individuals with Overweight/Obesity Humans
STUDY_SUMMARY
Objective: We sought to identify the circulating metabolites that would serve as markers of glucagon action. Design: In this study, we performed a continuous 72-hour glucagon infusion in healthy individuals with overweight/obesity. Participants were randomized to either glucagon (12.5 ng/kg/min) (GCG 12.5) or glucagon (25 ng/kg/min) GCG 25 or a placebo control were included. A comprehensive metabolomics analysis was then performed from plasma isolated at several time points during the infusion to identify markers of glucagon activity.
INSTITUTE
Translational Research Institute- AdventHealth Orlando
Identification of distinct metabolic perturbations and associated immunomodulatory events during intra-erythrocytic development stage of pediatric Plasmodium falciparum malaria (part-II)
STUDY_SUMMARY
The goal of this study was to interrogate biochemical profiles manifested in human serum samples originating from a cohort of West African children, collected before and during P. falciparum malarial infection, with the aim of characterizing metabolic migration associated with severity of malarial infection.
Identification of distinct metabolic perturbations and associated immunomodulatory events during intra-erythrocytic development stage of pediatric Plasmodium falciparum malaria (part-III)
STUDY_SUMMARY
The goal of this study was to interrogate biochemical profiles manifested in human serum samples originating from a cohort of West African children, collected before and during P. falciparum malarial infection, with the aim of characterizing metabolic migration associated with severity of malarial infection.
Perfluorooctanesulfonic acid (PFOS) and perfluorohexanesulfonic acid (PFHxS) alter the blood lipidome and the hepatic proteome in a murine model of diet-induced obesity
STUDY_SUMMARY
Perfluorooctanesulfonic acid (PFOS) and perfluorohexanesulfonic acid (PFHxS) alter the blood lipidome and the hepatic proteome in a murine model of diet-induced obesity
Mitochondrial health is enhanced in rats with higher vs. lower intrinsic exercise capacity and extended lifespan
STUDY_SUMMARY
The intrinsic aerobic capacity of an organism is thought to play a role in aging and longevity. Maximal respiratory rate capacity, a metabolic performance measure, is one of the best predictors of cardiovascular- and all-cause mortality. Rats selectively bred for high-(HCR) vs. low-(LCR) intrinsic running-endurance capacity have up to 31% longer lifespan. We found that positive changes in indices of mitochondrial health in cardiomyocytes (respiratory reserve, maximal respiratory capacity, resistance to mitochondrial permeability transition, autophagy/mitophagy, higher lipids-over-glucose utilization) are uniformly associated with the extended longevity in HCR vs. LCR female rats. Cross-sectional heart metabolomics revealed pathways from lipid metabolism in the heart which were significantly enriched by a select group of strain dependent metabolites, consistent with enhanced lipids utilization by HCR cardiomyocytes. Heart-liver-serum metabolomics further revealed shunting of lipidic substrates between liver and heart via serum during aging. Thus, mitochondrial health in cardiomyocytes is associated with extended longevity in rats with higher intrinsic exercise capacity, and likely these findings can be translated to other populations as predictors of outcomes of health and survival.
INSTITUTE
National Institute on Aging
DEPARTMENT
Cardioprotection Section
LABORATORY
Laboratory of Cardiovascular Science
LAST_NAME
Sollott
FIRST_NAME
Steven
ADDRESS
Laboratory of Cardiovascular Science, National Institute on Aging, NIH, Baltimore, MD 21224, USA
Aromatic amino acid metabolism by the anaerobic gut bacterium Clostridium sporogenes
STUDY_SUMMARY
Germ-free mice were mono-colonized with wild-type Clostridium sporogenes or its isogenic phenyllactate dehydratase (fldC) mutant. Feces, cecal contents, serum, and urine were collected for untargeted GC-TOF analysis.
Control (DMSO 0.1%; v/v) and 10 µM DRB18 treated A549 lung cancer cells in vitro for 48 hours
STUDY_TYPE
Anticancer compound treatment experiment
STUDY_SUMMARY
Control (DMSO 0.1%; v/v) and 10 µM DRB18 were used to treated 5 million A549 lung cancer cells in vitro for 48 hours. The untargeted metabolomics analysis was performed on the cell lysates. The main objective of the study was to determine changes in metabolite abundances in lung cancer after treatment with DRB18, an inhibitor of glucose transporter proteins.
INSTITUTE
Ohio University
DEPARTMENT
Biological Sciences
LABORATORY
Dr. Xiaozhuo Chen, Edison biotechnology Institute
LAST_NAME
Shriwas
FIRST_NAME
Pratik
ADDRESS
172 Water Tower, Building 25, The Ridges, Konnekar Research Centerm Athens Ohio - 45701, USA
Comparing gas chromatography with time-of-flight, quadrupole time-of-light and quadrupole mass spectrometry for stable isotope tracing
STUDY_SUMMARY
Stable isotope tracers are applied in vivo and in vitro studies to reveal the activity of enzymes and intracellular metabolic pathways. Most often, such tracers are used with gas chromatography coupled to mass spectrometry (GC-MS) due to its ease of operation and reproducible mass spectral databases. Differences in isotope tracer performance of classic GC-quadrupole MS instrument and newer time-of-flight instruments are not well-studied. Here, we used three commercially available instruments for the analysis of identical samples from a stable isotope labeling study that used [U-13C6] d-glucose to investigate the metabolism of Rothia mucilaginosa with respect to 29 amino acids and hydroxyl acids involved in primary metabolism. Overall, all three GC-MS instruments (low-resolution GC-SQ-MS, low-resolution GC-TOF-MS, and high-resolution GC-Q-TOF-MS) can be used to perform stable isotope tracing studies for glycolytic intermediates, TCA metabolites and amino acids, yielding similar biological results, with high-resolution GC-Q-TOF-MS offering additional capabilities to identify chemical structures of unknown compounds that might show significant isotope enrichments in biological studies.
INSTITUTE
University of California, Davis
LAST_NAME
Zhang
FIRST_NAME
Ying
ADDRESS
451 East Health Science Drive, Davis, CA, 95616, USA
Untargeted metabolomics of intestinal organoids treated with fructose
STUDY_TYPE
Metabolite profile and pathway analysis
STUDY_SUMMARY
We performed untargeted metabolomics of intestinal organoids treated with fructose (10 mM) for 24 hr.At the 5th day of secondary organoid culture, the organoids were treated with fructose (10 mM D-fructose)-containing IntestiCult organoid growth medium for 24 hr and washed with pre-cooled PBS before harvesting.
Isotope Tracing Analysis in Intestinal Organoids with fructose
STUDY_SUMMARY
We isolated and cultured Intestinal Organoids from Mouse. To trace the metabolism of fructose, intestinal organoids were cultured in unlabeled fructose-containing DMEM/F12 medium (10 mM D-fructose, 0 mM D-glucose, 2.5 mM L-glutamine) for 12 hr, and then switched into 13C labeled fructose-containing medium (10 mM U-[13C] D-fructose, Sigma-aldrich) for 6 hr.
Lipids were quantified in human plasma from the 1:3 matched TEDDY case-control subjects (Lee et al., 2013). Blood plasma was extracted following the methyl-tert-butyl ether (MTBE) extraction protocols. The choice of internal standards and chromatographic conditions was optimized by using toluene in the reconstitution solvent mixture to ensure that very lipophilic components like cholesteryl esters (CEs) and triacylglycerols (TAGs) are efficiently transferred to the ultrahigh-pressure liquid chromatography (UHPLC) column in the injection process. Lipids were analyzed by charged surface hybrid column electrospray ionization quadrupole time of flight tandem mass spectrometer (CSH-ESI QTOF MS/MS). The analytical ultra-high-pressure liquid chromatography (UHPLC) column is protected by a short guard column which was replaced after 400 injections while the UHPLC column was replaced after 1,200 serum (or plasma) extract injections. The sequence of column replacements were evaluated to ensure no detrimental effects were detected with respect to peak shapes, absolute or relative lipid retention times or reproducibility of quantifications. Automatic valve switching was used after each injection to reduce sample carryover for highly lipophilic compounds. This valve switching employed a dual solvent wash, first with a water/acetonitrile mixture (1:1, v/v) and subsequently with a 100% isopropanol wash. LC-BinBase was used as an untargeted approach for annotating chromatographic peaks and spectra against a dynamically built library of compounds. The quantified raw dataset was normalized by the SERRF bioinformatics pipeline [1]. In the LC-QTOF data, samples were removed before normalization if they failed the laboratory’s QC standards or were missing data for more than half of the compounds. The SERRF normalized data have been made available for identified compounds. Results data for unidentified compounds are available un-normalized. An explanation of the study design variables are explained in detail in a data dictionary provided in the raw data download section. References: 1) Lee HS, Burkhardt B, McLeod W, Smith S, Eberhard C, Lynch K, Hadley D, Rewers M, Simell O, She JX, Hagopian W, Lernmark A, Akolkar B, Ziegler AG, Krischer J, and the TEDDY Study Group: Biomarker discovery study design for type 1 diabetes in The Environmental Determinants of Diabetes in the Young (TEDDY) study. Diabetes/Metabolism Research and Reviews. Epub 2013 December 15. doi: 10.1002/dmrr.2510 (PubMed ID: 24339168). 2) Fan S, Kind T, Cajka T, Hazen SL, Tang WHW, Kaddurah-Daouk R, Irvin MR, Arnett DK, Barupal DK, Fiehn O: Systematic Error Removal Using Random Forest for Normalizing Large-Scale Untargeted Lipidomics Data. Anal Chem 2019, 91(5):3590-3596.
Remodeling Lipids in the Transition from Chronic Liver Disease to Hepatocellular Carcinoma (Blood) - part I
STUDY_SUMMARY
Comparing blood lipidomics of healthy volunteers to patients with chronic liver disease (CLD), and to patients with HCC caused by viral infections. We contrasted our findings in blood to lipid alterations in liver tumor and nontumor tissue samples from HCC patients.
INSTITUTE
West Coast Metabolomics Center - UC Davis
LAST_NAME
Ismail
FIRST_NAME
Israa
ADDRESS
451 Health Sciences Drive, Room 1313, Davis, CA, 95616, USA
Remodeling Lipids in the Transition from Chronic Liver Disease to Hepatocellular Carcinoma (Liver) - part II
STUDY_SUMMARY
Comparing blood lipidomics of healthy volunteers to patients with chronic liver disease (CLD), and to patients with HCC caused by viral infections. We contrasted our findings in blood to lipid alterations in liver tumor and nontumor tissue samples from HCC patients.
INSTITUTE
University of California, Davis
DEPARTMENT
West coast metabolomics center
LABORATORY
Fiehn lab
LAST_NAME
Ismail
FIRST_NAME
Israa
ADDRESS
451 health science drive, 95616 ,Davis, California, USA.
Deletion of the diabetes candidate gene Slc16a13 in mice
STUDY_SUMMARY
The metabolome of plasma and liver lysates of Slc16a13 knockout mice was analyzed. Genome-wide association studies identified SLC16A13 as novel target gene in type 2 diabetes. The SLC16A13 gene encodes for SLC16A13/MCT13, a member of the solute carrier 16 family of monocarboxylate transporters. So far, biology and physiological function of SLC16A13 is unknown. Deletion of Slc16a13 is hypothezised to affect intrahepatocellular monocarboxylate availability, that drives increased oxidative phosphorylation, while reducing hepatic lipid content, thereby attenuating hepatic insulin resistance.
INSTITUTE
West Coast Metabolomics Center - UC Davis
DEPARTMENT
Klinik für Diabetologie, Endokrinologie, Nephrologie
LABORATORY
Institut für Diabetesforschung und Metabolische Erkrankungen (IDM)
Urinary microbiota and metabolome in pediatric vesicoureteral reflux and scarring
STUDY_TYPE
Observational/cross-sectional
STUDY_SUMMARY
We enrolled girls and boys aged zero to nine years presenting to a pediatric urologist for recurrent urinary tract infection (UTI) or renal scarring (decreased uptake on a nuclear renal scan) or grade 3-5 vesico ureteral reflux (VUR). Exclusion criteria included other urogenital abnormalities, medical renal disease, immunodeficiency, syndromes associated with VUR, acute UTI, persistent UTI (ongoing positive urine culture 1-3 weeks after completing a treatment course), or global renal atrophy on imaging. At one patient visit, a urine specimen was collected for 16S and metabolomic analysis.
Mucosal-Associated-Invariant-T (MAIT) cells stimulated with IL-12/IL-12, anti-CD3/CD28 or both for 16 hours
STUDY_SUMMARY
The untargeted metabolomics analysis was performed after metabolite extraction from vital cells. The main object of the study was to define the activation of MAIT cells on the molecular level.
Metabolic profiling of plasma collected from Peromyscus leucopus and Mus musculus following LPS treatment
STUDY_TYPE
Untargeted Metabolomic profiling
STUDY_SUMMARY
Small molecule metabolites were extracted from plasma from Peromyscus leucopus and Mus musculus BALB/c and analyzed by liquid chromatography couple with mass spectrometry (LC-MS). XCMS software was used for peak picking, grouping and retention time correction from LC-MS data and generated a molecular feature spreadsheet. Pathway way enrichment analysis was carried out using Mummichog pathway analysis software using data from feature table.
E.coli K-12 treated by IPL_analysis of organic phase
STUDY_SUMMARY
In this study, E.coli K-12 was treated by intense pulsed light (IPL) for 0-20 seconds. Then the organic/lipid phase of the cellular metabolome was extracted and submitted to untargeted LC-MS based metabolomic study.
Identify putative volatile biomarkers of Coccidioides spp. grown in vitro
STUDY_TYPE
Untargeted metabolomics
STUDY_SUMMARY
Valley fever (coccidioidomycosis) is an endemic fungal pneumonia of the North and South American deserts. The causative agents of Valley fever are the dimorphic fungi Coccidioides immitis and C. posadasii, which grow as mycelia in the environment and spherules within the lungs of vulnerable hosts. The current diagnostics for Valley fever are severely lacking due to poor sensitivity and invasiveness, contributing to a 23-day median time-to-diagnosis, and therefore new diagnostic tools are needed. We are working toward the development of a breath-based diagnostic for coccidioidomycosis, and in this initial study we characterized the volatile metabolomes (or volatilomes) of in vitro cultures of Coccidioides. Using solid-phase microextraction and comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC×GC–TOFMS), we characterized the VOCs produced by six strains of each species during mycelial or spherule growth. We detected a total of 353 VOCs that were at least two-fold more abundant in a Coccidioides culture versus medium controls and found the volatile metabolome of Coccidioides is more dependent on growth phase (spherule versus mycelia) than on the species. The volatile profiles of C. immitis and C. posadasii have strong similarities, indicating that a single suite of Valley fever breath biomarkers can be developed to detect both species.
INSTITUTE
Arizona State University
DEPARTMENT
School of Life Sciences
LABORATORY
Bean Laboratory
LAST_NAME
Bean
FIRST_NAME
Heather
ADDRESS
PO Box 874501 Tempe, AZ 85287
EMAIL
Heather.D.Bean@asu.edu
PHONE
4807273395
PUBLICATIONS
Lifecycle dominates the volatilome character of the dimorphic fungus Coccidioides spp Emily A. Higgins Keppler, Heather L. Mead, Bridget M. Barker, Heather D. Bean bioRxiv 2021.01.15.426916; doi: https://doi.org/10.1101/2021.01.15.426916
Plasmodium falciparum metabolomics as a result of treatment with putative acetyl-CoA synthetase inhibitors
STUDY_SUMMARY
Plasmodium falciparum cells in culture were treated with respective compounds for 2.5 hours at 10xIC50 values. Metabolites were isolated using 90% methanol, dried, reconstituted in HPLC-grade water, and analyzed by HPLC/MS. Resulting data were analyzed and compiled to generate study data.
INSTITUTE
Pennsylvania State University
DEPARTMENT
Chemistry
LABORATORY
Llinás Laboratory
LAST_NAME
Llinás
FIRST_NAME
Manuel
ADDRESS
W126 Millennium Science Complex, University Park, PENNSYLVANIA, 16802, USA
E.coli K-12 treated by IPL - analysis of polar phase (part-II)
STUDY_SUMMARY
E.coli K-12 cells were treated by IPL, extracted and separated into organic/lipid phase and polar phase. Chemical derivatization with dansyl chloride was applied for analysis of amino acids in the polar phase extraction.
Branched-chain alpha-ketoacids are preferentially reaminated and activate protein synthesis in the rat heart
STUDY_SUMMARY
Branched-chain amino acids (BCAA) and their cognate α-ketoacids (BCKA) are elevated in an array of cardiometabolic diseases. Here we demonstrate that the major metabolic fate of uniformly-13C-labeled α-ketoisovalerate ([U-13C]KIV) in the heart is reamination to valine. Activation of cardiac branched-chain α-ketoacid dehydrogenase (BCKDH) by treatment with the BCKDH kinase inhibitor, BT2, does not impede the strong flux of [U-13C]KIV to valine.
Branched-chain alpha-ketoacids are preferentially reaminated and activate protein synthesis in the mouse heart
STUDY_SUMMARY
Branched-chain amino acids (BCAA) and their cognate α-ketoacids (BCKA) are elevated in an array of cardiometabolic diseases. Here we demonstrate that sequestration of BCAA and BCKA away from mitochondrial oxidation is likely due to low levels of expression of the mitochondrial BCAA transporter SLC25A44 in the heart, as its overexpression significantly lowers accumulation of [13C]-labeled valine from [U-13C]KIV.
NMR metabolomics analysis of ricin-induced and fasting hypoglycemia (part-II)
STUDY_SUMMARY
Mice were subjected to ricin exposure or fasting conditions for 2 hours, 8 hours, or an overnight period. Following treatment, livers were removed and metabolites were extracted and analyzed by NMR.
INSTITUTE
Montana State University
LAST_NAME
Kempa
FIRST_NAME
Jake
ADDRESS
103 Chemistry and Biochemistry Building, Bozeman, Montana, 59717, USA
Targeted Sphingolipid analysis of human Fibroblasts silenced for or overexpressing GOLPH3
STUDY_SUMMARY
A group of sequentially-acting enzymes operating at the branchpoint among sphingolipid synthetic pathways binds the Golgi-localised oncoprotein GOLPH3. GOLPH3 sorts these enzymes into vesicles for intra-Golgi retro-transport, acting as a component of the cisternae inter-conversion mechanisms. Through these effects, GOLPH3 controls the sub-Golgi localisation, and the lysosomal degradation rate of specific enzymes. Here we evaluated the impact of overexpressing or silencing GOLPH3 on the sphingolipid composition of dermal human fibroblasts by targeted lipid analysis.
Targeted Sphingolipid analysis of HeLa silenced for or overexpressing GOLPH3 or LCS
STUDY_SUMMARY
A group of sequentially-acting enzymes operating at the branchpoint among sphingolipid synthetic pathways binds the Golgi-localised oncoprotein GOLPH3. GOLPH3 sorts these enzymes into vesicles for intra-Golgi retro-transport, acting as a component of the cisternae inter-conversion mechanisms. Through these effects, GOLPH3 controls the sub-Golgi localisation, and the lysosomal degradation rate of specific enzymes. Here we evaluated the impact of overexpressing or silencing GOLPH3 or its client enzyme lactosylceramide synthase (LCS) on the sphingolipid composition of HeLa cells by targeted lipid analysis.
Untargeted phospholipid analysis of HeLa silenced for or overexpressing GOLPH3
STUDY_SUMMARY
A group of sequentially-acting enzymes operating at the branchpoint among sphingolipid synthetic pathways binds the Golgi-localised oncoprotein GOLPH3. GOLPH3 sorts these enzymes into vesicles for intra-Golgi retro-transport, acting as a component of the cisternae inter-conversion mechanisms. Through these effects, GOLPH3 controls the sub-Golgi localisation, and the lysosomal degradation rate of specific enzymes. Here we evaluated the impact of overexpressing or silencing GOLPH3 on the glycerophospholipid composition of HeLa cells by untargeted lipid analysis.
Untargeted urine LC-HRMS metabolomics profiling for bladder cancer binary outcome classification
STUDY_SUMMARY
Two samples cohorts were analysed for bladder cancer biomarkers selection. Untargeted urine RP UPLC-HRMS metabolomics profiling was utilized in SCAN MS mode and positive polarity. Dilute and shoot technique was employed for sample preparation.
A gut microbe-focused metabolomics pipeline enables mechanistic interrogation of microbiome metabolism.
STUDY_SUMMARY
Gut microbes modulate host phenotypes and are associated with numerous health effects in humans, ranging from cancer immunotherapy response to metabolic disease and obesity. However, difficulty in accurate and high-throughput functional analysis of human gut microbes has hindered defining mechanistic connections between individual microbial strains and host phenotypes. One key way the gut microbiome influences host physiology is through the production of small molecules hindered by limited tools calibrated to detect products of anaerobic biochemistry in the gut. Here we construct a microbiome-focused, integrated mass-spectrometry pipeline to accelerate the identification of microbiota-dependent metabolites (MDMs) in diverse sample types. We report the metabolic profiles of 178 gut microbe strains using our library of 833 metabolites. Leveraging this metabolomics resource we establish deviations in the relationships between phylogeny and metabolism, use machine learning to discover novel metabolism in Bacteroides, and employ comparative genomics-based discovery of candidate biochemical pathways. MDMs can be detected in diverse body fluids in gnotobiotic and conventional mice and traced back to corresponding metabolomic profiles of cultured bacteria. Collectively, our microbiome-focused metabolomics pipeline and interactive metabolomics profile explorer are a powerful tool for characterizing microbe and microbe-host interactions.
A cross-sectional study of functional and metabolic changes during aging through the lifespan in male mice (Muscle) part-I
STUDY_SUMMARY
Aging is associated with distinct phenotypical, physiological, and functional changes, leading to the onset of disease and death. The progression of aging-related traits varies widely among individuals, influenced by their environment, lifestyle, and genetics. In this study, we performed physiologic and functional tests cross-sectionally throughout the entire lifespan of male C57BL/6N mice. In parallel, metabolomics analyses in serum, brain, liver, heart, and skeletal muscle were also performed to identify signatures associated with frailty and age-dependent functional decline. Our findings indicate that the decline in gait speed as a function of age and frailty is associated with dramatic increases in the energetic cost of physical activity and decreases in working capacity. Aging and functional decline prompt organs to rewire their substrate selection and metabolism towards redox-related pathways, mainly in liver and heart. Collectively, the data provide a framework to further understand and characterize processes of aging at the individual and organ levels.
INSTITUTE
National Institutes of Health
DEPARTMENT
NIA
LABORATORY
Experimental Gerontology Section and Translational Gerontology Branch
LAST_NAME
de Cabo
FIRST_NAME
Rafael
ADDRESS
251 Bayview Blvd. Suite 100/Room 5C214. Baltimore, MD 21224
A cross-sectional study of functional and metabolic changes during aging through the lifespan in male mice (Serum) part-II
STUDY_SUMMARY
Aging is associated with distinct phenotypical, physiological, and functional changes, leading to the onset of disease and death. The progression of aging-related traits varies widely among individuals, influenced by their environment, lifestyle, and genetics. In this study, we performed physiologic and functional tests cross-sectionally throughout the entire lifespan of male C57BL/6N mice. In parallel, metabolomics analyses in serum, brain, liver, heart, and skeletal muscle were also performed to identify signatures associated with frailty and age-dependent functional decline. Our findings indicate that the decline in gait speed as a function of age and frailty is associated with dramatic increases in the energetic cost of physical activity and decreases in working capacity. Aging and functional decline prompt organs to rewire their substrate selection and metabolism towards redox-related pathways, mainly in liver and heart. Collectively, the data provide a framework to further understand and characterize processes of aging at the individual and organ levels.
INSTITUTE
National Institutes of Health
DEPARTMENT
NIA
LABORATORY
Experimental Gerontology Section and Translational Gerontology Branch
LAST_NAME
de Cabo
FIRST_NAME
Rafael
ADDRESS
251 Bayview Blvd. Suite 100/Room 5C214. Baltimore, MD 21224
A cross-sectional study of functional and metabolic changes during aging through the lifespan in male mice (Heart) part-IV
STUDY_SUMMARY
Aging is associated with distinct phenotypical, physiological, and functional changes, leading to the onset of disease and death. The progression of aging-related traits varies widely among individuals, influenced by their environment, lifestyle, and genetics. In this study, we performed physiologic and functional tests cross-sectionally throughout the entire lifespan of male C57BL/6N mice. In parallel, metabolomics analyses in serum, brain, liver, heart, and skeletal muscle were also performed to identify signatures associated with frailty and age-dependent functional decline. Our findings indicate that the decline in gait speed as a function of age and frailty is associated with dramatic increases in the energetic cost of physical activity and decreases in working capacity. Aging and functional decline prompt organs to rewire their substrate selection and metabolism towards redox-related pathways, mainly in liver and heart. Collectively, the data provide a framework to further understand and characterize processes of aging at the individual and organ levels.
INSTITUTE
National Institutes of Health
DEPARTMENT
NIA
LABORATORY
Experimental Gerontology Section and Translational Gerontology Branch
LAST_NAME
de Cabo
FIRST_NAME
Rafael
ADDRESS
251 Bayview Blvd. Suite 100/Room 5C214. Baltimore, MD 21224
A cross-sectional study of functional and metabolic changes during aging through the lifespan in male mice (Brain) part-V
STUDY_SUMMARY
Aging is associated with distinct phenotypical, physiological, and functional changes, leading to the onset of disease and death. The progression of aging-related traits varies widely among individuals, influenced by their environment, lifestyle, and genetics. In this study, we performed physiologic and functional tests cross-sectionally throughout the entire lifespan of male C57BL/6N mice. In parallel, metabolomics analyses in serum, brain, liver, heart, and skeletal muscle were also performed to identify signatures associated with frailty and age-dependent functional decline. Our findings indicate that the decline in gait speed as a function of age and frailty is associated with dramatic increases in the energetic cost of physical activity and decreases in working capacity. Aging and functional decline prompt organs to rewire their substrate selection and metabolism towards redox-related pathways, mainly in liver and heart. Collectively, the data provide a framework to further understand and characterize processes of aging at the individual and organ levels.
INSTITUTE
National Institutes of Health
DEPARTMENT
NIA
LABORATORY
Experimental Gerontology Section and Translational Gerontology Branch
LAST_NAME
de Cabo
FIRST_NAME
Rafael
ADDRESS
251 Bayview Blvd. Suite 100/Room 5C214. Baltimore, MD 21224
Sclerostin antibody increases trabecular bone and bone mechanical properties by increasing osteoblast activity damaged by whole-body irradiation in mice
STUDY_TYPE
Basic research
STUDY_SUMMARY
Irradiation therapy causes bone deterioration and increased risk for skeletal-related events. Irradiation interferes with trabecular architecture through increased osteoclastic activity, decreased osteoblastic activity, and increased adipocyte expansion in the bone marrow (BM), which further compounds bone-related disease. Neutralizing antibodies to sclerostin (Scl-Ab) increase bone mass and strength by increasing bone formation and reducing bone resorption. We hypothesized that treatment with Scl-Ab would attenuate the adverse effects of irradiation by increasing bone volume and decreasing BM adipose tissue (BMAT), resulting in better quality bone. In this study, 12-week-old female C57BL/6J mice were exposed to 6 Gy whole-body irradiation or were non-irradiated, then administered Scl-Ab (25 mg/kg) or vehicle weekly for 5 weeks. Femoral µCT analysis confirmed that the overall effect of IR significantly decreased trabecular bone volume/total volume (Tb.BV/TV) (2-way ANOVA, p<0.0001) with a -43.8% loss in Tb.BV/TV in the IR control group. Scl-Ab independently increased Tb.BV/TV by 3.07-fold in non-irradiated and 3.6-fold in irradiated mice (2-way ANOVA, p<0.0001). Irradiation did not affect cortical parameters, although Scl-Ab increased cortical thickness and area significantly in both irradiated and non-irradiated mice (2-way ANOVA, p<0.0001). Femoral mechanical testing confirmed Scl-Ab significantly increased bending rigidity and ultimate moment independently of irradiation (2-way ANOVA, p<0.0001). Static and dynamic histomorphometry of the femoral metaphysis revealed osteoblast vigor, not number, was significantly increased in the irradiated mice treated with Scl-Ab. Systemic alterations were assessed through serum lipidomic analysis, which showed that Scl-Ab normalized lipid profiles in the irradiated group. This data supports the theory of sclerostin as a novel contributor to the regulation of osteoblast activity after irradiation. Overall, our data support the hypothesis that Scl-Ab ameliorates the deleterious effects of whole-body irradiation on bone and adipose tissue in a mouse model. Our findings suggest that future research into localized and systemic therapies after irradiation exposure is warranted.
Machine learning-enabled renal cell carcinoma status prediction using multi-platform urine-based metabolomics
STUDY_SUMMARY
Currently, Renal Cell Carcinoma (RCC) is identified through expensive cross-sectional imaging, frequently followed by renal mass biopsy, which is invasive and subject to sampling errors. Hence, there is a critical need for a non-invasive diagnostic assay. RCC is a disease of altered cellular metabolism with the tumor(s) in close proximity to the urine in the kidney suggesting metabolomic profiling would be an excellent choice for assay development. Here, we applied liquid chromatography-mass spectrometry (LC-MS), nuclear magnetic resonance (NMR), and machine learning (ML) for the discovery of candidate metabolic panels for RCC. The study cohort consists of 82 RCC patients and 174 healthy controls, these were separated into two sub-cohorts: model cohort and the test cohort. Discriminatory metabolic features were selected in the model cohort, using univariate, wrapper, and embedded methods of feature selection. Three ML techniques with different induction biases were used for training and hyperparameter tuning. Final assessment of RCC status prediction was made using the test cohort with the selected biomarkers and the tuned ML algorithms. A seven-metabolite panel consisting of endogenous and exogenous metabolites enabled the prediction of RCC with 88% accuracy, 94% sensitivity, and 85% specificity in the test cohort, with an AUC of 0.98.
Lipid Profiling of Mouse Intestinal Organoids for studying APC Mutations
STUDY_SUMMARY
Inactivating mutations including both germline and somatic mutations in the adenomatous polyposis coli (APC) gene drives most familial and sporadic colorectal cancers. Understanding the metabolic implications of this mutation will aid to establish its wider impact on cellular behaviour and potentially inform clinical decisions. However, to date, alterations in lipid metabolism induced by APC mutations remain unclear. Intestinal organoids have gained widespread popularity in studying colorectal cancer and chemotherapies, because their three-dimensional structure more accurately mimics an in vivo environment. Here, we aimed to investigate intra-cellular lipid disturbances induced by APC gene mutations in intestinal organoids using a reversed-phase ultra-high-performance liquid chromatography mass spectrometry (RP-UHPLC-MS)-based lipid profiling method. Lipids of the organoids grown from either wildtype (WT) or mice with Apc mutations (Lgr5–EGFP-IRES-CreERT2 Apcfl/fl) were extracted and analysed using RP-UHPLC-MS. Concentrations of phospholipids (e.g. PC(16:0/16:0), PC(18:1/20:0), PC(38:0), PC(18:1/22:1)), ceramides (e.g. Cer(d18:0/22:0), Cer(d42:0), Cer(d18:1/24:1)) and hexosylceramide (e.g. HexCer(d18:1/16:0), HexCer(d18:1/22:0)) were higher in Apcfl/fl organoids, whereas levels of sphingomyelins (e.g. SM(d18:1/14:0), SM(d18:1/16:0) ) were lower compared to WT. These observations indicate that cellular metabolism of sphingomyelin was upregulated, resulting in the cellular accumulation of ceramides and production of HexCer due to the absence of Apcfl/fl in the organoids. Our observations demonstrated lipid profiling of organoids and provided an enhanced insight into the effects of the APC mutations on lipid metabolism, making for a valuable addition to screening options of the organoid lipidome.
SARS-CoV-2 infection rewires host cell metabolism and is potentially susceptible to mTORC1 inhibition
STUDY_SUMMARY
Viruses hijack host cell metabolism to acquire the building blocks required for viral replication. Understanding how SARS-CoV-2 alters host cell metabolism could lead to potential treatments for COVID-19, the disease caused by SARS-CoV-2 infection. Here we profile metabolic changes conferred by SARS-CoV-2 infection in kidney epithelial cells and lung air-liquid interface cultures and show that SARS-CoV-2 infection increases glucose carbon entry into the TCA cycle via increased pyruvate carboxylase expression. SARS-CoV-2 also reduces host cell oxidative glutamine metabolism while maintaining reductive carboxylation. Consistent with these changes in host cell metabolism, we show that SARS-CoV-2 increases activity of mTORC1, a master regulator of anabolic metabolism, in cell lines and patient lung stem cell-derived airway epithelial cells. We also show evidence of mTORC1 activation in COVID-19 patient lung tissue. Notably, mTORC1 inhibitors reduce viral replication in kidney epithelial cells and patient-derived lung stem cell cultures. This suggests that targeting mTORC1 could be a useful antiviral strategy for SARS-CoV-2 and treatment strategy for COVID-19 patients, although further studies are required to determine the mechanism of inhibition and potential efficacy in patients.
Metabolic signatures of NAFLD - Lipidomics data (part 1 of 3)
STUDY_SUMMARY
Serum samples were randomized and extracted using a modified version of the previously-published Folch procedure, as applied recently [20]. The maternal samples were analysed as one batch and the cord blood samples as a second batch. In short, 10 µL of 0.9% NaCl and, 120 µL of CHCl3: MeOH (2:1, v/v) containing the internal standards (c = 2.5 µg/mL) was added to 10 µL of each serum sample. The standard solution contained the following compounds: 1,2-diheptadecanoyl-sn-glycero-3-phosphoethanolamine (PE(17:0/17:0)), N-heptadecanoyl-D-erythro-sphingosylphosphorylcholine (SM(d18:1/17:0)), N-heptadecanoyl-D-erythro-sphingosine (Cer(d18:1/17:0)), 1,2-diheptadecanoyl-sn-glycero-3-phosphocholine (PC(17:0/17:0)), 1-heptadecanoyl-2-hydroxy-sn-glycero-3-phosphocholine (LPC(17:0)) and 1-palmitoyl-d31-2-oleoyl-sn-glycero-3-phosphocholine (PC(16:0/d31/18:1)), were purchased from Avanti Polar Lipids, Inc. (Alabaster, AL, USA), and, triheptadecanoylglycerol (TG(17:0/17:0/17:0)) was purchased from Larodan AB (Solna, Sweden). The samples were vortex mixed and incubated on ice for 30 min after which they were centrifuged (9400 × g, 3 min). 60 µL from the lower layer of each sample was then transferred to a glass vial with an insert and 60 µL of CHCl3: MeOH (2:1, v/v) was added to each sample. The samples were stored at -80 °C until analysis. Calibration curves using 1-hexadecyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine (PC(16:0e/18:1(9Z))), 1-(1Z-octadecenyl)-2-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine (PC(18:0p/18:1(9Z))), 1-stearoyl-2-hydroxy-sn-glycero-3-phosphocholine (LPC(18:0)), 1-oleoyl-2-hydroxy-sn-glycero-3-phosphocholine (LPC(18:1)), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (PE(16:0/18:1)), 1-(1Z-octadecenyl)-2-docosahexaenoyl-sn-glycero-3-phosphocholine (PC(18:0p/22:6)) and 1-stearoyl-2-linoleoyl-sn-glycerol (DG(18:0/18:2)), 1-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine (LPE(18:1)), N-(9Z-octadecenoyl)-sphinganine (Cer(d18:0/18:1(9Z))), 1-hexadecyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine (PE(16:0/18:1)) from Avanti Polar Lipids, 1-Palmitoyl-2-Hydroxy-sn-Glycero-3-Phosphatidylcholine (LPC(16:0)), 1,2,3 trihexadecanoalglycerol (TG(16:0/16:0/16:0)), 1,2,3-trioctadecanoylglycerol (TG(18:0/18:0/18:)) and 3β-hydroxy-5-cholestene-3-stearate (ChoE(18:0)), 3β-Hydroxy-5-cholestene-3-linoleate (ChoE(18:2)) from Larodan, were prepared to the following concentration levels: 100, 500, 1000, 1500, 2000 and 2500 ng/mL (in CHCl3:MeOH, 2:1, v/v) including 1250 ng/mL of each internal standard. The samples were analyzed by ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UHPLC-QTOFMS). Briefly, the UHPLC system used in this work was a 1290 Infinity II system from Agilent Technologies (Santa Clara, CA, USA). The system was equipped with a multi sampler (maintained at 10 °C), a quaternary solvent manager and a column thermostat (maintained at 50 °C). Injection volume was 1 µL and the separations were performed on an ACQUITY UPLC® BEH C18 column (2.1 mm × 100 mm, particle size 1.7 µm) by Waters (Milford, MA, USA). The mass spectrometer coupled to the UHPLC was a 6545 QTOF from Agilent Technologies interfaced with a dual jet stream electrospray (Ddual ESI) ion source. All analyses were performed in positive ion mode and MassHunter B.06.01 (Agilent Technologies) was used for all data acquisition. Quality control was performed throughout the dataset by including blanks, pure standard samples, extracted standard samples and control serum samples, including in-house serum and a pooled QC with an aliquot of each sample was collected and pooled and used as quality control sample. Relative standard deviations (% RSDs) for identified lipids in the control serum samples (n = 13) and in the pooled serum samples (n = 54) were on average 22.4% and 17.5%, respectively.
INSTITUTE
Örebro University
LAST_NAME
McGlinchey
FIRST_NAME
Aidan
ADDRESS
School of Medical Sciences, Örebro, Örebro, 70281, Sweden
Metabolic signatures of NAFLD - Polar metabolomics data (part II)
STUDY_SUMMARY
Analysis of polar metabolites Serum samples were randomized and sample preparation was carried out as described previously (Castilloet al. 2011). In summary, 400 μL of MeOH containing ISTDs (heptadecanoic acid, deuterium-labeled DL-valine, deuterium-labeled succinic acid, and deuterium-labeled glutamic acid, c = 1 µg/mL) was added to 30 µl of the serum samples which were vortex mixed and incubated on ice for 30 min after which they were centrifuged (9400 × g, 3 min) and 350 μL of the supernatant was collected after centrifugation. The solvent was evaporated to dryness and 25 μL of MOX reagent was added and the sample was incubated for 60 min at 45 °C. 25 μL of MSTFA was added and after 60 min incubation at 45 °C 25 μL of the retention index standard mixture (n-alkanes, c=10 µg/mL) was added. The analyses were carried out on an Agilent 7890B GC coupled to 7200 QTOF MS. Injection volume was 1 µL with 100:1 cold solvent split on PTV at 70 °C, heating to 300 °C at 120 °C/minute. Column: Zebron ZB-SemiVolatiles. Length: 20m, I.D. 0.18mm, film thickness: 0.18 µm. With initial Helium flow 1.2 mL/min, increasing to 2.4 mL/min after 16 mins. Oven temperature program: 50 °C (5 min), then to 270°C at 20 °C/min and then to 300 °C at 40 °C/min (5 min). EI source: 250 °C, 70 eV electron energy, 35µA emission, solvent delay 3 min. Mass range 55 to 650 amu, acquisition rate 5 spectra/s, acquisition time 200 ms/spectrum. Quad at 150 °C, 1.5 mL/min N2 collision flow, aux-2 temperature: 280 °C. Calibration curves were constructed using alanine, citric acid, fumaric acid, glutamic acid, glycine, lactic acid, malic acid, 2-hydroxybutyric acid, 3-hydroxybutyric acid, linoleic acid, oleic acid, palmitic acid, stearic acid, cholesterol, fructose, glutamine, indole-3-propionic acid, isoleucine, leucine, proline, succinic acid, valine, asparagine, aspartic acid, arachidonic acid, glycerol-3-phosphate, lysine, methionine, ornithine, phenylalanine, serine and threonine purchased from Sigma-Aldrich (St. Louis, MO, USA) at concentration range of 0.1 to 80 μg/mL. An aliquot of each sample was collected and pooled and used as quality control samples, together with a NIST SRM 1950 serum sample and an in-house pooled serum sample. Relative standard deviations (% RSDs) of the metabolite concentrations in control serum samples showed % RSDs within accepted analytical limits at averages of 27.2% and 29.2% for in-house QC abd pooled QC samples.
INSTITUTE
Örebro University
LAST_NAME
McGlinchey
FIRST_NAME
Aidan
ADDRESS
School of Medical Sciences, Örebro, Örebro, 70281, Sweden
Large-scale enzyme-based xenobiotic identification for exposomics
STUDY_TYPE
Xenobiotic Metabolism
STUDY_SUMMARY
Exposomics methods are limited by low abundance of xenobiotic metabolites and lack of authentic standards, which precludes identification using solely mass spectrometry-based criteria. Here, we validate a method for enzymatic generation of xenobiotic metabolites for use with high-resolution mass spectrometry for chemical identification. Generated xenobiotic metabolites were used to confirm identities of respective metabolites in mice and human samples based upon accurate mass, retention time, and co-occurrence with related xenobiotic metabolites. The data shared here are high-resolution Orbitrap MS data for S9 incubations of 140 xenobiotic compounds with 0 and 24 hour time points for all reactions.
Phospholipid transfer function of PTPIP51 at mitochondria-associated ER membranes
STUDY_SUMMARY
In eukaryotic cells, mitochondria are closely tethered to the endoplasmic reticulum (ER) at sites called mitochondria-associated ER membranes (MAMs). Ca2+ ion and phospholipid transfer occurs at MAMs to support diverse cellular functions. Unlike those in yeast, the protein complexes involved in phospholipid transfer at MAMs in humans have not been identified. Here, we determined the crystal structure of the tetratricopeptide repeat domain of PTPIP51 (PTPIP51_TPR), a mitochondrial protein that interacts with the ER-anchored VAPB protein at MAMs. The structure of PTPIP51_TPR showed an archetypal TPR fold, and an electron density corresponding to an unidentified lipid-like molecule probably derived from the protein expression host was found in the structure. We revealed functions of PTPIP51 in phospholipid binding/transfer, particularly of phosphatidic acid, in vitro. Depletion of PTPIP51 in cells reduced the mitochondrial cardiolipin level. Additionally, we confirmed that the PTPIP51–VAPB interaction is mediated by the FFAT-like motif of PTPIP51 and the MSP domain of VAPB. Our findings suggest that PTPIP51 is a phospholipid transfer protein with a MAM-tethering function similar to the ERMES complex in yeast.
INSTITUTE
Korea Basic Science Institute
DEPARTMENT
Western Seoul Center
LABORATORY
Integrated Metabolomics Research Group
LAST_NAME
Lee
FIRST_NAME
Jueun
ADDRESS
150, Bugahyeon-ro, Seodaemun-gu, Seoul, Republic of Korea (Zip code: 03759)
The effects of birth weight and breeding value for protein deposition on the plasma metabolome in growing pigs (part-II)
STUDY_SUMMARY
An experiment was conducted with growing pigs, to determine the effects of birth weight (BiW) and estimated breeding value for protein deposition (EBV) on the metabolomic profile in plasma samples collected under different dietary regimens: protein adequate (A) or protein restricted (R, 70% of A).
INSTITUTE
Aarhus University
DEPARTMENT
Animal Science
LABORATORY
Metabolomics LC-MS platform Aarhus University Foulum
Mitochondrial ATP fuels ABC transporter-mediated drug efflux in cancer chemoresistance
STUDY_SUMMARY
Chemotherapy remains the standard of care for most cancers worldwide, however development of chemoresistance due to the presence of the drug-effluxing ABC transporters remains a significant problem. The development of safe and effective means to overcome chemoresistance is critical for achieving durable remissions in many cancer patients. We have investigated the energetic demands of ABC transporters in the context of the metabolic adaptations of chemoresistant cancer cells. Here we show that ABC transporters use mitochondrial-derived ATP as a source of energy to efflux drugs out of cancer cells. We further demonstrate that the loss of MCJ (DnaJC15), an endogenous negative regulator of mitochondrial respiration, in chemoresistant cancer cells boosts their ability to produce ATP from mitochondria and fuel ABC transporters. We have developed novel MCJ mimetics that can attenuate mitochondrial respiration and safely overcome chemoresistance in vitro and in vivo. Administration of MCJ mimetics in combination with standard chemotherapeutic drugs could therefore become an new strategy for treatment of multiple cancers.
INSTITUTE
University of Colorado Denver
DEPARTMENT
Biochemistry and Molecular Genetics
LABORATORY
Angelo D'Alessandro
LAST_NAME
Culp-Hill
FIRST_NAME
Rachel
ADDRESS
12801 E 17th Ave L18-9403D, Aurora, Colorado, 80045, USA
Mitochondrial ATP fuels ABC transporter-mediated drug efflux in cancer chemoresistance (part-II)
STUDY_SUMMARY
Chemotherapy remains the standard of care for most cancers worldwide, however development of chemoresistance due to the presence of the drug-effluxing ABC transporters remains a significant problem. The development of safe and effective means to overcome chemoresistance is critical for achieving durable remissions in many cancer patients. We have investigated the energetic demands of ABC transporters in the context of the metabolic adaptations of chemoresistant cancer cells. Here we show that ABC transporters use mitochondrial-derived ATP as a source of energy to efflux drugs out of cancer cells. We further demonstrate that the loss of MCJ (DnaJC15), an endogenous negative regulator of mitochondrial respiration, in chemoresistant cancer cells boosts their ability to produce ATP from mitochondria and fuel ABC transporters. We have developed novel MCJ mimetics that can attenuate mitochondrial respiration and safely overcome chemoresistance in vitro and in vivo. Administration of MCJ mimetics in combination with standard chemotherapeutic drugs could therefore become an new strategy for treatment of multiple cancers.
INSTITUTE
University of Colorado Denver
DEPARTMENT
Biochemistry and Molecular Genetics
LABORATORY
Angelo D'Alessandro
LAST_NAME
Culp-Hill
FIRST_NAME
Rachel
ADDRESS
12801 E 17th Ave L18-9403D, Aurora, Colorado, 80045, USA
Mitochondrial ATP fuels ABC transporter-mediated drug efflux in cancer chemoresistance (part-III)
STUDY_SUMMARY
Chemotherapy remains the standard of care for most cancers worldwide, however development of chemoresistance due to the presence of the drug-effluxing ABC transporters remains a significant problem. The development of safe and effective means to overcome chemoresistance is critical for achieving durable remissions in many cancer patients. We have investigated the energetic demands of ABC transporters in the context of the metabolic adaptations of chemoresistant cancer cells. Here we show that ABC transporters use mitochondrial-derived ATP as a source of energy to efflux drugs out of cancer cells. We further demonstrate that the loss of MCJ (DnaJC15), an endogenous negative regulator of mitochondrial respiration, in chemoresistant cancer cells boosts their ability to produce ATP from mitochondria and fuel ABC transporters. We have developed novel MCJ mimetics that can attenuate mitochondrial respiration and safely overcome chemoresistance in vitro and in vivo. Administration of MCJ mimetics in combination with standard chemotherapeutic drugs could therefore become an new strategy for treatment of multiple cancers.
Understanding systemic and local inflammation induced by nasal polyposis: role of the allergic phenotype (part-I)
STUDY_SUMMARY
Chronic rhinosinusitis with nasal polyps (CRSwNP) is characterized by persistent symptoms associated to the development of nasal polyps. To this day, the molecular mechanisms involved are still not well defined. However, it has been suggested that a sustained inflammation as allergy is involved in its onset. In this pilot study, we aimed to look into the effect of the allergic status of the patient and in their underlying mechanisms. To achieve this, we recruited 22 patients with CRSwNP and classified them in non-allergic and allergic using ImmunoCAP ISAC molecular diagnosis. Plasma samples were analyzed using liquid chromatography coupled to mass spectrometry (LC-MS). Subsequently, the identified changed metabolites from plasma that were commercially available were then analyzed by targeted analysis in some nasal polyps. Additionally, nasal polyp and mucosa tissue samples were examined for eosinophils and neutrophils. We found that 9 out of the 22 patients were sensitized to some aeroallergens (named as allergic). The other 13 patients had no sensitizations (non-allergic). Regarding metabolomics, we found that bilirubin, cortisol, lysophosphatidylcholines (LPCs) 16:0, 18:0 and 20:4 and lysophosphatidylinositol (LPI) 20:4, metabolites that are usually related to a sustained allergic inflammation, were unexpectedly increased in the plasma of non-allergic patients with CRSwNP compared to allergic patients with CRSwNP. LPC 16:0, LPC 18:0 and LPI 20:4 metabolites followed the same trend in the nasal polyp as they did in plasma. Comparison of nasal polyps with nasal mucosa tissue showed a significant increase in eosinophils (p < 0.001) and neutrophils (p < 0.01) in allergic patients with CRSwNP. There were also more eosinophils in the polyps of non-allergic patients with CRSwNP than in their nasal mucosa (p <0.01). The polyps from non-allergic patients with CRSwNP had less eosinophils than the polyps of allergic patients with CRSwNP (p < 0.05). Our data suggests that there is a systemic inflammatory response associated to CRSwNP in the absence of allergy, which could be accountable for the nasal polyp development. Allergic patients with CRSwNP presented a higher number of eosinophils located in nasal polyps suggesting that eosinophilia might be connected to the development of nasal polyps in these patients.
INSTITUTE
CEMBIO
LAST_NAME
Delgado Dolset
FIRST_NAME
María Isabel
ADDRESS
Urb. Montepríncipe s/n, Ctra. Boadilla del Monte km 5.3, Madrid, Madrid, 28668, Spain
The COVIDome Explorer Researcher Portal (Red Blood Cells)
STUDY_SUMMARY
COVID-19 pathology involves dysregulation of diverse molecular, cellular, and physiological processes. In order to expedite integrated and collaborative COVID-19 research, we completed multi-omics analysis of hospitalized COVID-19 patients including matched analysis of the whole blood transcriptome, plasma proteomics with two complementary platforms, cytokine profiling, plasma and red blood cell metabolomics, deep immune cell phenotyping by mass cytometry, and clinical data annotation. We refer to this multidimensional dataset as the COVIDome. We then created the COVIDome Explorer, an online researcher portal where the data can be analyzed and visualized in real time. We illustrate here the use of the COVIDome dataset through a multi-omics analysis of biosignatures associated with C-reactive protein (CRP), an established marker of poor prognosis in COVID-19, revealing associations between CRP levels and damage-associated molecular patterns, depletion of protective serpins, and mitochondrial metabolism dysregulation. We expect that the COVIDome Explorer will rapidly accelerate data sharing, hypothesis testing, and discoveries worldwide.
COVID-19 pathology involves dysregulation of diverse molecular, cellular, and physiological processes. In order to expedite integrated and collaborative COVID-19 research, we completed multi-omics analysis of hospitalized COVID-19 patients including matched analysis of the whole blood transcriptome, plasma proteomics with two complementary platforms, cytokine profiling, plasma and red blood cell metabolomics, deep immune cell phenotyping by mass cytometry, and clinical data annotation. We refer to this multidimensional dataset as the COVIDome. We then created the COVIDome Explorer, an online researcher portal where the data can be analyzed and visualized in real time. We illustrate here the use of the COVIDome dataset through a multi-omics analysis of biosignatures associated with C-reactive protein (CRP), an established marker of poor prognosis in COVID-19, revealing associations between CRP levels and damage-associated molecular patterns, depletion of protective serpins, and mitochondrial metabolism dysregulation. We expect that the COVIDome Explorer will rapidly accelerate data sharing, hypothesis testing, and discoveries worldwide.
Mice homozygous for the Scd1ab-2J allele have a defect Scd1 gene with an in-frame stop codon in exon 2. To identify SCD1-derived phospholipid species, we analysed PI and PC species in organs and tissues that highly express SCD1 and are considered as targets for intervention with SCD1 inhibitors, i.e., liver, skin, hind leg skeletal muscle, and white abdominal fat.
The Role of Intestinal-derived FGF15 and Vertical Sleeve Gastrectomy on Plasma Bile Acid Composition in Mice
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Bariatric surgeries such as the Vertical Sleeve Gastrectomy (VSG) are invasive but provide the most effective long-term metabolic improvements in individuals with obesity and/or Type 2 diabetes. These powerful effects of manipulating the gastrointestinal tract point to an important role of gastrointestinal signals in regulating both energy balance and metabolism. To that end, we have used mouse models of VSG to identify key gut signals that mediate these beneficial effects. Previous data from our rodent model of VSG led us to hypothesize a potential role for the hormone Fibroblast-Growth Factor15/19 (mouse/human ortholog) which pharmacologically can regulate many aspects of energy homeostasis and glucose handling. FGF15 is expressed in ileal enterocytes of the small intestine and is released postprandially. Like many other gut hormones, postprandial plasma concentrations of the human ortholog FGF19 and ileal FGF15 expression in mice increase after VSG. We generated intestinal-specific FGF15 knock out (VilCreERT2; Fgf15f/f) mice and controls, which were maintained on 60% high-fat diet. VSG resulted in increased plasma bile acid levels. However, intestinal-specific FGF15 knock out mice had considerably higher levels of circulating total and hydrophobic bile acids after VSG. Unlike what we had predicted, intestinal-specific FGF15 knock out mice lost more weight after VSG as a result of increased lean tissue loss compared to control mice. Further, the loss of bone mineral density and bone marrow adipose tissue observed after VSG in control mice was even greater in intestinal-specific FGF15 knock out mice, perhaps secondary to anemia and elevated erythropoietin/FGF23. Finally the effect of VSG to improve glucose tolerance and to reduce hepatic cholesterol was also absent in intestinal-specific FGF15 knock out mice. These data point to an important role for intestinal FGF15 to protect the organism from deleterious effects of bile acid toxicity after VSG.
X13CMS: Global Tracking of Isotopic Labels in Untargeted Metabolomics
STUDY_TYPE
Untargeted metabolomics
STUDY_SUMMARY
Studies of isotopically labeled compounds have been fundamental to understanding metabolic pathways and fluxes. They have traditionally, however, been used in conjunction with targeted analyses that identify and quantify a limited number of labeled downstream metabolites. Here we describe an alternative workflow that leverages recent advances in untargeted metabolomic technologies to track the fates of isotopically labeled metabolites in a global, unbiased manner. This untargeted approach can be applied to discover novel biochemical pathways and characterize changes in the fates of labeled metabolites as a function of altered biological conditions such as disease. To facilitate the data analysis, we introduce X13CMS, an extension of the widely used mass spectrometry-based metabolomic software package XCMS. X13CMS uses the XCMS platform to detect metabolite peaks and perform retention-time alignment in liquid chromatography/mass spectrometry (LC/MS) data. With the use of the XCMS output, the program then identifies isotopologue groups that correspond to isotopically labeled compounds. The retrieval of these groups is done without any a priori knowledge besides the following input parameters: (i) the mass difference between the unlabeled and labeled isotopes, (ii) the mass accuracy of the instrument used in the analysis, and (iii) the estimated retention-time reproducibility of the chromatographic method. Despite its name, X13CMS can be used to track any isotopic label. Additionally, it detects differential labeling patterns in biological samples collected from parallel control and experimental conditions. We validated the ability of X13CMS to accurately retrieve labeled metabolites from complex biological matrices both with targeted LC/MS/MS analysis of a subset of the hits identified by the program and with labeled standards spiked into cell extracts. We demonstrate the full functionality of X13CMS with an analysis of cultured rat astrocytes treated with uniformly labeled (U-)13C-glucose during lipopolysaccharide (LPS) challenge. Our results show that out of 223 isotopologue groups enriched from U-13C-glucose, 95 have statistically significant differential labeling patterns in astrocytes challenged with LPS compared to unchallenged control cells. Only two of these groups overlap with the 32 differentially regulated peaks identified by XCMS, indicating that X13CMS uncovers different and complementary information from untargeted metabolomic studies. Like XCMS, X13CMS is implemented in R. It is available from our laboratory website at http://pattilab.wustl.edu/x13cms.php.
INSTITUTE
Washington University, St. Louis
LAST_NAME
Cho
FIRST_NAME
Kevin
ADDRESS
1 Brookings Drive, Campus Box 1134, St. Louis, MO, 63130, USA
Metabolomic profiling of the rat hippocampus across developmental ages and after learning
STUDY_TYPE
Developmental study
STUDY_SUMMARY
Little is known about how the hippocampal metabolomic profile changes across development and in response to learning at different ages. To fill this knowledge gap, we employed an untargeted metabolomic analyses in rats to determine how the hippocampal metabolome changes over the course of post-natal development under basal conditions and following inhibitory avoidance (IA) training, an aversive episodic event. We found that unique metabolomic profiles accompany learning at different ages. Subsequent biochemical and behavioral studies based on unique metabolomic regulations in the infant hippocampus established that infantile learning selectively recruits the glutathione-mediated antioxidant defenses for the formation of infantile memory.
Lung metabolomics after ischemic acute kidney injury reveals increased oxidative stress, altered energy production, and ATP depletion
STUDY_SUMMARY
Acute kidney injury (AKI) is a complex disease associated with increased mortality that may be due to deleterious distant organ effects. AKI associated with respiratory complications, in particular, has a poor outcome. In murine models, AKI is characterized by increased circulating cytokines, lung chemokine upregulation, and neutrophilic infiltration, similar to other causes of indirect acute lung injury (ALI)(e.g., sepsis). Many causes of lung inflammation are associated with a lung metabolic profile characterized by increased oxidative stress, a shift towards the use of other forms of energy production, and/or a depleted energy state. To our knowledge, there are no studies that have evaluated pulmonary energy production and metabolism after AKI. We hypothesized that based on the parallels between inflammatory acute lung injury and AKI-mediated lung injury, a similar metabolic profile would be observed. Lung metabolomics and ATP levels were assessed 4 hours, 24 hours, and 7 days after ischemic AKI in mice. Numerous novel findings regarding the effect of AKI on the lung were observed including 1) increased oxidative stress, 2) a shift toward alternate methods of energy production, and 3) depleted levels of ATP. The findings in this report bring to light novel characteristics of AKI-mediated lung injury and provide new leads into the mechanisms by which AKI in patients predisposes to pulmonary complications.
Increasing evidence indicates that physical activity and exercise training may delay or prevent the onset of Alzheimer’s disease (AD). However, systemic biomarkers that can measure exercise effects on brain function and that link to relevant metabolic responses are lacking. This study utilized blood samples of 23 asymptomatic late middle-aged adults with familial and genetic risk for AD who underwent 26 weeks of supervised treadmill training. Metabolomic profiles were evaluated using MS.
INSTITUTE
University of Wisconsin - Madison
DEPARTMENT
Medicine
LABORATORY
Wisconsin Alzheimer's Disease Research Center
LAST_NAME
Gaitán
FIRST_NAME
Julian
ADDRESS
600 Highland Ave. J5/1M CSC MC2420, Madison, WI 53792
Gut microbiome influence on metabolic 1 disease in HIV and high-risk populations
STUDY_SUMMARY
Poor metabolic health, characterized by insulin resistance and dyslipidemia, is higher in people living with HIV (PLWH) and has been linked with inflammation, anti-retroviral therapy (ART) drugs, and ART-associated lipodystrophy (LD). Metabolic disease is associated with gut microbiome composition outside the context of HIV but has not been deeply explored in HIV infection nor in high-risk men who have sex with men (HR-MSM), who have a highly altered gut microbiome composition. Furthermore, the contribution of increased bacterial translocation and associated systemic inflammation that has been described in HIV-positive and HR-MSM individuals has not been explored. We used a multi-omic approach to explore relationships between gut microbes, immune phenotypes, diet, and metabolic health across ART-treated PLWH with and without LD; untreated PLWH; and HR-MSM. For PLWH on ART, we further explored associations with the plasma metabolome.
Multi-omics analysis of glucose-mediated signaling by a moonlighting Gβ protein Asc1/RACK1
STUDY_TYPE
Untargeted UPLC-MS Metabolomics Analysis
STUDY_SUMMARY
While much is known about glucose metabolism in yeast, less is known about the receptors and signaling pathways that indicate glucose availability. We obtained metabolic profiles for wildtype and 16 mutants affecting the yeast glucose sensing pathway, comparing 0.05% glucose vs 10 min after glucose addition to 2%. First, we determined that the G protein-coupled receptor (Gpr1/Gpa2) directs early events in glucose utilization while the transceptors (Snf3/Rgt2) regulate subsequent processes and downstream products of glucose metabolism. Whereas the large G protein transmits the signal from its cognate receptor, Ras2 (but not Ras1) integrates responses from both receptor pathways. Second, we determined the relative contributions of the G protein α (Gpa2) and β (Asc1) subunits to glucose-initiated processes. We determined that Gpa2 is primarily involved in regulating carbohydrate metabolism while Asc1 is primarily involved in amino acid metabolism. Both proteins are involved in regulating purine metabolism. Collectively, our analysis reveals the molecular basis for glucose detection and the earliest events of glucose-dependent signal transduction in yeast.
INSTITUTE
University of North Carolina at Chapel Hill
DEPARTMENT
Nutrition
LABORATORY
Metabolomics and Exposome Laboratory, Nutrition Research Institute, UNC Chapel Hill
LAST_NAME
Sumner
FIRST_NAME
Susan
ADDRESS
500 Laureate Way, Nutrition Research Institute, UNC Chapel Hill
GC-XLE method development: dSPE and MgSO4 as clean-up for sample preparation
STUDY_TYPE
Untargeted MS anlaysis
STUDY_SUMMARY
Compared to using dispersive SPE (dSPE) based on the QuEChERS procedure, we found similar reproducibility using high purity MgSO4 to analyze standard reference material (SRM) of human serum and human plasma samples and slightly higher recovery of targeted chemicals using MgSO4. To avoid contamination by environmental chemicals in solvents and reagents used for QuEChERS, we chose to use high purity MgSO4 to remove water-soluble interferences.
INSTITUTE
Emory University
DEPARTMENT
Medicine/Pulmonary
LABORATORY
Dean Jones
LAST_NAME
Hu
FIRST_NAME
Xin
ADDRESS
Emory University Whitehead building (Rm 225), 615 Michael Street
Metabolomics Analysis of Time-Series Gastrointestinal Lumen Samples
STUDY_SUMMARY
Samples were retrieved from a human small intestine samples over 8 hours. Metabolomics analysis followed resulting in many annotated metabolites. Intensity profiles gives insight into gastrointestinal functions.
Changes in mesenteric lymph lipid profile of mice upon high-fat diet with and without Celecoxib (part I)
STUDY_SUMMARY
Untargeted lipid profiling of mesenteric mice lymph from mice fed with CHOW, HFD and HFD supplemented with COx-2 inhibitor drug Celecoxib. It is proposed that Celecoxib can protect from deleterious morphological changes in lymphatic system caused by obesity/HFD.
INSTITUTE
Monash Institute of Pharmaceutical Sciences
DEPARTMENT
Drug Delivery, Disposition and Dynamics
LABORATORY
Trevaskis Lab, Creek Lab
LAST_NAME
Anderson
FIRST_NAME
Dovile
ADDRESS
6 Anderson
EMAIL
dovile.anderson@gmail.com
NUM_GROUPS
3
TOTAL_SUBJECTS
26
NUM_MALES
26
PUBLICATIONS
Manuscript NATMETAB-A20022406A Mesenteric lymphatic dysfunction promotes insulin resistance and represents a potential novel treatment target in obesity
Changes in mesenteric lymph lipid profile of mice upon high-fat diet with and without Celecoxib
STUDY_TYPE
Untargeted lipidomics analysis
STUDY_SUMMARY
Untargeted lipid profiling of mesenteric mice lymph from mice fed with CHOW, HFD and HFD supplemented with COx-2 inhibitor drug Celecoxib. It is proposed that Celecoxib can protect from deleterious morphological changes in lymphatic system caused by obesity due to HFD.
INSTITUTE
Monash Institute of Pharmaceutical Sciences
DEPARTMENT
Drug Delivery, Disposition and Dynamics
LABORATORY
Trevaskis Lab, Creek Lab
LAST_NAME
Anderson
FIRST_NAME
Dovile
ADDRESS
6 Anderson
EMAIL
dovile.anderson@gmail.com
PHONE
8671141
NUM_GROUPS
4
TOTAL_SUBJECTS
20
NUM_MALES
20
PUBLICATIONS
Manuscript NATMETAB-A20022406A Mesenteric lymphatic dysfunction promotes insulin resistance and represents a potential novel treatment target in obesity
We tested XLE quantification of chemicals in a non-fortified reference material: SRM-1957. Results show that XLE detected 29 out of 32 chemicals with certified or estimated reference values in the ng/kg range in SRM-1957; 16 out of 29 chemicals were quantified at >65% of the reference levels.
INSTITUTE
Emory University
DEPARTMENT
Medicine/Pulmonary
LABORATORY
Dean Jones
LAST_NAME
Hu
FIRST_NAME
Xin
ADDRESS
Emory University Whitehead building (Rm 225), 615 Michael Street
We evaluated quantification using XLE by testing 68 different chemicals (PCB, PBDEs, chlorinated pesticides) in SRM-1958 using external calibration curves (0.05 to 2 ng/mL) and comparing measured values to the reference concentrations reported for SRM. We identified all 40 PCBs that are reported with a reference mass fraction (including certified values and non-certified estimates) in the range of 46.6 to 490 ng/kg in SRM-1958 certificate of analysis (issue date: 11 October 2018). Quantification without adjustment for recovery was reproducible with 29 PCB qualifications at >70% and 35 PCBs at >65% of the reference levels. Eleven out of 13 PBDE/PBBs and all 17 organochlorine pesticides were identifiable and reproducibly quantified in this experiment. Therefore, XLE provides sufficient recovery to support accurate absolute quantification of a broad range of environmental chemicals. Overall, XLE supported measurement of 68 out of the 70 chemicals that are in the ng/kg range in SRM-1958.
INSTITUTE
Emory University
DEPARTMENT
Medicine/Pulmonary
LABORATORY
Dean Jones
LAST_NAME
Hu
FIRST_NAME
Xin
ADDRESS
Emory University Whitehead building (Rm 225), 615 Michael Street
Validation of XLE quantification using standard reference material. High recovery of [13C] labelled chemicals was obtained for important classes of environmental chemicals (PCB, PBDE, PAH, chlorinated pesticides) in NIST SRM-1957. Recoveries ranged from 110±7% for [13C10]mirex to 91 to 105% for congeners of universally [13C] labeled PCBs, PBDEs and chlorinated pesticides, with only [13C12]p,p’-dichlorodiphenyldichloroethylene (p,p’-DDE) having low recovery of 65±6%. Therefore, the simplified extraction procedure provides an efficient recovery of environment chemicals in an organic phase.
INSTITUTE
Emory University
DEPARTMENT
Medicine/Pulmonary
LABORATORY
Dean Jones
LAST_NAME
Hu
FIRST_NAME
Xin
ADDRESS
Emory University Whitehead building (Rm 225), 615 Michael Street
We tested the general utility of XLE in a variety of human biological samples by analyzing human lung and thyroid tissues and stool samples. We quantified 32 environmental chemicals in 11 human lungs, with HCB, PCB-28 and PCB-18 being most frequently detected (10 out of 11). The commonly detected chemicals in human plasma were detected less frequently in the lung. For the 11 lungs, p,p’-DDE was detected in eight, PCB-153 in five, PBDE-47 and PCB-138 in four and PCB-180 in three. Although the plasma samples were from non-diseased individuals and the lungs were both diseased and non-diseased individuals, HCA results suggest that environmental chemical profiles in human lung may be very different from plasma.
INSTITUTE
Emory University
DEPARTMENT
Medicine/Pulmonary
LABORATORY
Dean Jones
LAST_NAME
Hu
FIRST_NAME
Xin
ADDRESS
Emory University Whitehead building (Rm 225), 615 Michael Street
In the small number of thyroids that was analyzed with XLE, 14 environmental chemicals were quantified. The most prevalent was p,p’-DDE, detected in 4 out of 5 thyroid samples, with median concentration (2.20 ng/g). The amounts of individual chemicals were highly variable among the individuals, and the small number of samples precludes any generalization. Nevertheless, HCA of correlation matrix showed high correlation of chemicals measured in the thyroid samples was similar to that in the lung and plasma.
INSTITUTE
Emory University
DEPARTMENT
Medicine/Pulmonary
LABORATORY
Dean Jones
LAST_NAME
Hu
FIRST_NAME
Xin
ADDRESS
Emory University Whitehead building (Rm 225), 615 Michael Street
Human stool samples, as a noninvasive matrix, have unique value in exposome research but have not been extensively studied for environmental chemical exposures. For lipophilic and unabsorbed dietary environmental chemicals, stool is a primary route of elimination and can therefore provide useful information on body burden and clearance of chemicals. In a pilot analysis of six human stool samples, we detected 52 and quantified 21 environmental chemicals, with HCB found in all samples. Quantification of HCB showed a median concentration of 0.057 ng/g. HCA of correlation matrix showed co-exposures of chemicals are likely as shown in the plasma, lung and thyroid. The high correlations of these persistent chemicals are not surprising as they likely derive from similar environmental exposure events.
INSTITUTE
Emory University
DEPARTMENT
Medicine/Pulmonary
LABORATORY
Dean Jones
LAST_NAME
Hu
FIRST_NAME
Xin
ADDRESS
Emory University Whitehead building (Rm 225), 615 Michael Street
Metabolic responses of two pioneer wood decay fungi to diurnally cycling temperature
STUDY_SUMMARY
1. Decomposition of lignin-rich wood by fungi drives nutrient recycling in woodland ecosystems. Fluctuating abiotic conditions are known to promote the functioning of ecological communities and ecosystems. In the context of wood decay, fluctuating temperature increases decomposition rates. Metabolomics, in tandem with other ‘omics tools, can highlight the metabolic processes affected by experimental treatments, even in the absence of genome sequences and annotations. Globally, natural wood decay communities are dominated by the phylum Basidiomycota. We examined the metabolic responses of Mucidula mucida, a dominant constituent of pioneer communities in beech branches in British woodlands, and Exidia glandulosa, a stress-selected constituent of the same communities, in response to constant and diurnally cycling temperature. 2. We applied untargeted metabolomics and proteomics to beech wood blocks, colonised by M. mucida or E. glandulosa and exposed to either diurnally cycling (mean 15 ± 10°C) or constant (15°C) temperature, in a fully factorial design. 3. Metabolites and proteins linked to lignin breakdown, the citric acid cycle, pentose phosphate pathway, carbohydrate metabolism, fatty acid metabolism and protein biosynthesis and turnover were under-enriched in fluctuating, compared to stable temperatures, in the generalist M. mucida. Conversely E. glandulosa showed little differential response to the experimental treatments. 4. Synthesis. By demonstrating temperature dependant metabolic signatures related to nutrient acquisition in a generalist wood decay fungus, we provide new insights into how abiotic conditions can affect community-mediated decomposition and carbon turnover in forests. We show that mechanisms underpinning important biogeochemical processes can be highlighted using untargeted metabolomics and proteomics in the absence of well-annotated genomes.
INSTITUTE
Swansea University
DEPARTMENT
Biosciences
LABORATORY
Fungal Molecular Ecology
LAST_NAME
Eastwood
FIRST_NAME
Daniel
ADDRESS
Wallace 102, Biosciences, College of Science, Swansea University, Swansea, SA2 8PP
Metabolomics-driven identification of biochemical mechanisms underlying the neuroprotective effects of pleiotrophin in a mouse model of Parkinson’s disease
STUDY_SUMMARY
Pleiotrophin (PTN) is a cytokine involved in nerve tissue repair processes, neuroinflammation and neuronal survival. PTN expression levels are upregulated in the nigrostriatal pathway of Parkinson’s Disease (PD) patients. We aimed to characterize the dopaminergic injury and glial activation in the nigrostriatal pathway of mice with transgenic Ptn overexpression in the brain (Ptn-Tg) after intrastriatal injection of the Parkinsonian toxin 6-hydroxydopamine (6-OHDA). The injection of 6-OHDA induced a significant decrease of the number of tyrosine hydroxylase (TH)-positive neurons in the substantia nigra and of the striatal TH contents in Wild type (Wt) mice. In contrast, these effects of 6-OHDA were blocked in Ptn-Tg mice. 6-OHDA injection did not cause robust changes in microglia but induced an exacerbated astrocytic response in Wt mice compared with Ptn-Tg mice. In metabolomics studies, we detected interesting metabolites that significantly discriminate the more injured 6-OHDA-injected Wt striatum and the more protected 6-OHDA-injected Ptn-Tg striatum. Particularly, we detected groups of metabolites, mostly corresponding to phospholipids, whose trends were opposite in both groups. In summary, the data confirm the neuroprotective effect of brain PTN overexpression in this mouse model of PD. New lipid-related PD drug candidates emerge from this study and the data presented here support the increasingly recognized “lipid cascade” in PD.
Evidence that class I glutamine amidotransferase, GAT1_2.1, acts as a glutaminase in roots of Arabidopsis thaliana
STUDY_TYPE
Targeted Metabolite Quantification
STUDY_SUMMARY
In this study, we used Arabidopsis root extracts, spiked with amide nitrogen labeled (15N1) Glutamine and a purified recombinant protein, both full length and glutaminase domain only versions, to determine the amido group acceptor, if any, in the glutamine amidotransferase reaction.
Searching for prognostic biomarkers of Parkinson´s Disease development in the Spanish EPIC cohort through a multiplatform metabolomics approach
STUDY_SUMMARY
The lack of knowledge about the onset and progression of Parkinson’s disease (PD) hampers its early diagnosis and treatment. We used a multiplatform untargeted metabolomics-based approach to uncover the biochemical remodeling induced by PD in a really early and pre-symptomatic stage and unveiling early potential diagnostic biomarkers. Baseline pre-clinical plasma samples (Pre-PD n=39; control group n=39) were obtained from the European Prospective Study on Nutrition and Cancer (EPIC) cohort, which healthy volunteers were followed for around 15 years to ascertain incident PD. Our finding revealed alterations in fatty acids metabolism, mitochondrial dysfunction, oxidative stress, and gut-brain axis dysregulation. This study is of inestimable value since this is the first study conducted with samples collected many years before the disease development.
INSTITUTE
Universidad CEU San Pablo
LAST_NAME
Gonzalez-Riano
FIRST_NAME
Carolina
ADDRESS
km 0, Universidad CEU-San Pablo Urbanización Montepríncipe. M-501, 28925 Alcorcón
The RNA-binding protein RBP42 regulates cellular energy metabolism in mammalian-infective Trypanosoma brucei
STUDY_SUMMARY
Metabolic changes following two days of RBP42 knockdown was investigated using a targeted metabolomics approach, designed to capture intermediary metabolites in central carbon metabolism including glycolytic intermediates, TCA compounds, amino acids, nucleotides and derivatives, were obtained using hydrophilic interaction liquid chromatography (HILIC) separation method coupled with mass spectrometry run in negative ionization mode
INSTITUTE
Rutgers University
LAST_NAME
Das
FIRST_NAME
Anish
ADDRESS
Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, Newark, NJ 07103
Metabolomic and lipidomic profiles of CKD in obese patients in serum and urine (part 1 of 3)
STUDY_TYPE
Human nephropathy in CKD obese patients
STUDY_SUMMARY
Obesity is a global pandemic with an increase prevalence over the years. This condition elevates the risk of developing cardiovascular diseases, hypertension and renal pathologies, like chronic kidney disease (CKD). In the present study, the metabolomic and the lipidomic profiles of CKD obese patients were analyzed comparing with obese subjects without CKD. Subsequently, CKD obese patients underwent bariatric surgery and the effect of surgery in the CKD progression of these subjects was evaluated. Serum and urine were measured by LC-MS and GC-HRAM equipment.
INSTITUTE
University Rey Juan Carlos
DEPARTMENT
Basics Science of Health
LAST_NAME
Lanzon
FIRST_NAME
Borja
ADDRESS
Avenida de Atenas S/N
EMAIL
borja.lanzon@urjc.es
PHONE
663692554
NUM_GROUPS
3
TOTAL_SUBJECTS
36
STUDY_COMMENTS
Serum LC-MS data: part 1 of 3. Samples were analyzed per duplicated.
Metabolomic and lipidomic profiles of CKD in obese patients in serum and urine (part 2 of 3)
STUDY_SUMMARY
Obesity is a global pandemic with an increase prevalence over the years. This condition elevates the risk of developing cardiovascular diseases, hypertension and renal pathologies, like chronic kidney disease (CKD). In the present study, the metabolomic and the lipidomic profiles of CKD obese patients were analyzed comparing with obese subjects without CKD. Subsequently, CKD obese patients underwent bariatric surgery and the effect of surgery in the CKD progression of these subjects was evaluated. Serum and urine were measured by LC-MS and GC-HRAM equipment.
INSTITUTE
University Rey Juan Carlos
DEPARTMENT
Basics Science of Health
LAST_NAME
Lanzon
FIRST_NAME
Borja
ADDRESS
Avenida de Atenas S/N, Alcorcón, Madrid, 28922, Spain
Metabolomic and lipidomic profiles of CKD in obese patients in serum and urine (part 3 of 3)
STUDY_SUMMARY
Obesity is a global pandemic with an increase prevalence over the years. This condition elevates the risk of developing cardiovascular diseases, hypertension and renal pathologies, like chronic kidney disease (CKD). In the present study, the metabolomic and the lipidomic profiles of CKD obese patients were analyzed comparing with obese subjects without CKD. Subsequently, CKD obese patients underwent bariatric surgery and the effect of surgery in the CKD progression of these subjects was evaluated. Serum and urine were measured by LC-MS and GC-HRAM equipment.
INSTITUTE
University Rey Juan Carlos
DEPARTMENT
Basics Science of Health
LAST_NAME
Lanzon
FIRST_NAME
Borja
ADDRESS
Avenida de Atenas S/N, Alcorcón, Madrid, 28922, Spain
The pregnancy metabolome from a multi-ethnic pregnancy cohort
STUDY_SUMMARY
The PRogramming of Intergenerational Stress Mechanisms (PRISM) study is an urban, ethnically diverse pregnancy cohort that was designed to study a range of chemical and non-chemical stressors in relation to maternal health, pregnancy outcomes, and child development. Pregnant women were enrolled from Boston and New York City hospitals and affiliated prenatal clinics beginning in 2011. Eligibility criteria included English or Spanish-speaking, over 18 years of age at enrollment, and singleton pregnancy. Exclusion criteria included HIV+ status or self-reported drinking ≥7 alcoholic drinks per week before pregnancy or any alcohol after pregnancy recognition
Reversing Epigenetic Gene Silencing to Overcome Immune Evasion in CNS Malignancies
STUDY_SUMMARY
Glioblastoma is an aggressive brain malignancy with a dismal prognosis. With emerging evidence that disproves the immune privileged environment in the brain, there is much interest in examining various immunotherapy strategies to treat these incurable cancers. Unfortunately, to date, clinical studies investigating immunotherapy regimens have not provided much evidence of efficacy, leading to questions about the suitability of immunotherapy strategies for these tumors. Inadequate inherent populations of lymphocytes in tumor (TILs) and limited trafficking of systemic circulating T cells into the central nervous system (CNS) likely contribute to the poor response to immunotherapy treatment for primary CNS cancers. This paucity of TILs is in concert with the finding of epigenetic silencing of genes that promote immune cell movement (chemotaxis) to the tumor. In this study we evaluated the ability of GSK126, a blood-brain barrier permeable small molecule inhibitor of EZH2, to reverse the epigenetic silencing of chemokines like CXCL9 and CXCL10. When combined with anti-PD-1 treatment, these IFN driven chemokines promote T cell infiltration, resulting in decreased tumor growth and enhanced survival in immunocompetent murine sub-cutaneous and intracranial tumor syngeneic models of GBM. Examination of the tumor micro-environment revealed that the decrease in tumor growth in the mice treated with the drug combination was accompanied by increased tumor CD8 T cell infiltration along with higher IFN expression. Additionally, a significant increase in CXCR3+ T cells in the draining lymph nodes was also found. Taken together, our data suggests that in glioblastoma, epigenetic modulation using GSK126 could improve current immunotherapy strategies by reversing the epigenetic changes that enable immune cell evasion leading to enhanced immune cell trafficking to the tumor.
Metabolomics of lung microdissections reveals region- and sex-specific metabolic effects of acute naphthalene exposure in mice (part I)
STUDY_SUMMARY
Naphthalene is a ubiquitous environmental contaminant produced by combustion of fossil fuels and is a primary constituent of both mainstream and side stream tobacco smoke. Naphthalene elicits region-specific toxicity in airway club cells through cytochrome P450 (P450)-mediated bioactivation, resulting in depletion of glutathione and subsequent cytotoxicity. While effects of naphthalene in mice have been extensively studied, few experiments have characterized global metabolomic changes in the lung. In individual lung regions, we found metabolomic changes in microdissected mouse lung conducting airways and parenchyma obtained from animals sacrificed 2, 6, and 24 hours following naphthalene treatment. Data on 577 unique identified metabolites were acquired by accurate mass spectrometry-based assays focusing on lipidomics and non-targeted metabolomics of hydrophilic compounds. Statistical analyses revealed distinct metabolite profiles between the two major lung regions. In addition, the number and magnitude of statistically significant exposure-induced changes in metabolite abundance were different between lung airways and parenchyma for unsaturated lysophosphatidylcholines (LPCs), dipeptides, purines, pyrimidines, and amino acids. Importantly, temporal changes were found to be highly distinct for male and female mice, with males exhibiting predominant treatment-specific changes only at two hours post-exposure. In females, metabolomic changes persisted until six hours post-naphthalene treatment, which may explain the previously characterized higher susceptibility of female mice to naphthalene toxicity. In both males and females, treatment-specific changes corresponding to lung remodeling, oxidative stress response, and DNA damage were observed, which may provide insights into potential mechanisms contributing to the previously reported effects of naphthalene exposure in the lung.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome Center
LABORATORY
Fiehn Lab
LAST_NAME
Stevens
FIRST_NAME
Nathanial C.
ADDRESS
451 Health Sciences Drive University of California Davis Davis, CA 95616
Metabolomics of lung microdissections reveals region- and sex-specific metabolic effects of acute naphthalene exposure in mice (part II)
STUDY_SUMMARY
Naphthalene is a ubiquitous environmental contaminant produced by combustion of fossil fuels and is a primary constituent of both mainstream and side stream tobacco smoke. Naphthalene elicits region-specific toxicity in airway club cells through cytochrome P450 (P450)-mediated bioactivation, resulting in depletion of glutathione and subsequent cytotoxicity. While effects of naphthalene in mice have been extensively studied, few experiments have characterized global metabolomic changes in the lung. In individual lung regions, we found metabolomic changes in microdissected mouse lung conducting airways and parenchyma obtained from animals sacrificed 2, 6, and 24 hours following naphthalene treatment. Data on 577 unique identified metabolites were acquired by accurate mass spectrometry-based assays focusing on lipidomics and non-targeted metabolomics of hydrophilic compounds. Statistical analyses revealed distinct metabolite profiles between the two major lung regions. In addition, the number and magnitude of statistically significant exposure-induced changes in metabolite abundance were different between lung airways and parenchyma for unsaturated lysophosphatidylcholines (LPCs), dipeptides, purines, pyrimidines, and amino acids. Importantly, temporal changes were found to be highly distinct for male and female mice, with males exhibiting predominant treatment-specific changes only at two hours post-exposure. In females, metabolomic changes persisted until six hours post-naphthalene treatment, which may explain the previously characterized higher susceptibility of female mice to naphthalene toxicity. In both males and females, treatment-specific changes corresponding to lung remodeling, oxidative stress response, and DNA damage were observed, which may provide insights into potential mechanisms contributing to the previously reported effects of naphthalene exposure in the lung.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome Center
LABORATORY
Fiehn Lab
LAST_NAME
Stevens
FIRST_NAME
Nathanial C.
ADDRESS
451 Health Sciences Drive University of California Davis Davis, CA 95616
Identification of unique metabolite networks between Latino and Caucasian patients with nonalcoholic fatty liver disease (NAFLD) (part II)
STUDY_SUMMARY
Nonalcoholic fatty liver disease (NAFLD) is a spectrum of liver pathology ranging from simple steatosis to nonalcoholic steatohepatitis (NASH); the latter is characterized by inflammation and fibrosis. Risk factors for NALFD include obesity, diabetes, hyperlipidemia, and hypertension—all of which are features of metabolic syndrome. NAFLD is a very heterogeneous disease, as it presents in different patterns in males and females and in patients from different ethnicities, with unclear predictors for development and severity of disease. Previous studies have shown that NAFLD is 1.4 times more frequent in Hispanics than in Caucasians. One of the major challenges in NAFLD is the lack of accurate, noninvasive biomarkers for the detection of the most aggressive presentation, NASH. The gold standard for the diagnosis is liver biopsy, which is an invasive procedure associated with possible complications. Noninvasive diagnosis of NASH is a major unmet medical need and there are no ethnicity-specific biomarkers that can diagnose this condition and predict its progression. Therefore, the main gap in knowledge that this proposal and line of research will address is the characterizing the different plasma and liver metabolomics profile of patients with fatty liver from two ethnicities (Latinos vs. Caucasians) and of both sexes. The overall hypothesis of the present study is that the higher incidence of nonalcoholic fatty liver (NAFL) in Latino patients is reflected in a different plasma and liver metabolomics profile compared to Caucasian patients with further sex-related differences. Characterization of metabolite networks can aid in identifying the mechanistic underpinnings of sex and ethnic driven differences in NAFL which could help diagnose and establish a prognosis of this condition, especially in the critical transition from NAFL to the more aggressive nonalcoholic steatohepatitis (NASH).To address this hypothesis, plasma metabolomics profile of samples from male and female Latino and Caucasian bariatric surgery patients with NAFL and from healthy subjects will be compared. Metabolomics findings will be related with liver pathology and liver transcriptome profiles from intraoperatively obtained liver biopsies using correlation, network, and pathway analysis.
INSTITUTE
University of California, Davis
DEPARTMENT
Department of Internal Medicine, Division of Gastroenterology and Hepatology
LABORATORY
Medici Lab
LAST_NAME
Medici
FIRST_NAME
Valentina
ADDRESS
4150 V Street - PSSB Suite 3500 - 95817 Sacramento CA
Identification of unique metabolite networks between Latino and Caucasian patients with nonalcoholic fatty liver disease (NAFLD) (part III)
STUDY_SUMMARY
Nonalcoholic fatty liver disease (NAFLD) is a spectrum of liver pathology ranging from simple steatosis to nonalcoholic steatohepatitis (NASH); the latter is characterized by inflammation and fibrosis. Risk factors for NALFD include obesity, diabetes, hyperlipidemia, and hypertension—all of which are features of metabolic syndrome. NAFLD is a very heterogeneous disease, as it presents in different patterns in males and females and in patients from different ethnicities, with unclear predictors for development and severity of disease. Previous studies have shown that NAFLD is 1.4 times more frequent in Hispanics than in Caucasians. One of the major challenges in NAFLD is the lack of accurate, noninvasive biomarkers for the detection of the most aggressive presentation, NASH. The gold standard for the diagnosis is liver biopsy, which is an invasive procedure associated with possible complications. Noninvasive diagnosis of NASH is a major unmet medical need and there are no ethnicity-specific biomarkers that can diagnose this condition and predict its progression. Therefore, the main gap in knowledge that this proposal and line of research will address is the characterizing the different plasma and liver metabolomics profile of patients with fatty liver from two ethnicities (Latinos vs. Caucasians) and of both sexes. The overall hypothesis of the present study is that the higher incidence of nonalcoholic fatty liver (NAFL) in Latino patients is reflected in a different plasma and liver metabolomics profile compared to Caucasian patients with further sex-related differences. Characterization of metabolite networks can aid in identifying the mechanistic underpinnings of sex and ethnic driven differences in NAFL which could help diagnose and establish a prognosis of this condition, especially in the critical transition from NAFL to the more aggressive nonalcoholic steatohepatitis (NASH).To address this hypothesis, plasma metabolomics profile of samples from male and female Latino and Caucasian bariatric surgery patients with NAFL and from healthy subjects will be compared. Metabolomics findings will be related with liver pathology and liver transcriptome profiles from intraoperatively obtained liver biopsies using correlation, network, and pathway analysis.
INSTITUTE
University of California, Davis
DEPARTMENT
Department of Internal Medicine, Division of Gastroenterology and Hepatology
LABORATORY
Medici Lab
LAST_NAME
Medici
FIRST_NAME
Valentina
ADDRESS
4150 V Street - PSSB Suite 3500 - 95817 Sacramento CA
Identification of unique metabolite networks between Latino and Caucasian patients with nonalcoholic fatty liver disease (NAFLD) (part IV)
STUDY_SUMMARY
Nonalcoholic fatty liver disease (NAFLD) is a spectrum of liver pathology ranging from simple steatosis to nonalcoholic steatohepatitis (NASH); the latter is characterized by inflammation and fibrosis. Risk factors for NALFD include obesity, diabetes, hyperlipidemia, and hypertension—all of which are features of metabolic syndrome. NAFLD is a very heterogeneous disease, as it presents in different patterns in males and females and in patients from different ethnicities, with unclear predictors for development and severity of disease. Previous studies have shown that NAFLD is 1.4 times more frequent in Hispanics than in Caucasians. One of the major challenges in NAFLD is the lack of accurate, noninvasive biomarkers for the detection of the most aggressive presentation, NASH. The gold standard for the diagnosis is liver biopsy, which is an invasive procedure associated with possible complications. Noninvasive diagnosis of NASH is a major unmet medical need and there are no ethnicity-specific biomarkers that can diagnose this condition and predict its progression. Therefore, the main gap in knowledge that this proposal and line of research will address is the characterizing the different plasma and liver metabolomics profile of patients with fatty liver from two ethnicities (Latinos vs. Caucasians) and of both sexes. The overall hypothesis of the present study is that the higher incidence of nonalcoholic fatty liver (NAFL) in Latino patients is reflected in a different plasma and liver metabolomics profile compared to Caucasian patients with further sex-related differences. Characterization of metabolite networks can aid in identifying the mechanistic underpinnings of sex and ethnic driven differences in NAFL which could help diagnose and establish a prognosis of this condition, especially in the critical transition from NAFL to the more aggressive nonalcoholic steatohepatitis (NASH).To address this hypothesis, plasma metabolomics profile of samples from male and female Latino and Caucasian bariatric surgery patients with NAFL and from healthy subjects will be compared. Metabolomics findings will be related with liver pathology and liver transcriptome profiles from intraoperatively obtained liver biopsies using correlation, network, and pathway analysis.
INSTITUTE
University of California, Davis
DEPARTMENT
Department of Internal Medicine, Division of Gastroenterology and Hepatology
LABORATORY
Medici Lab
LAST_NAME
Medici
FIRST_NAME
Valentina
ADDRESS
4150 V Street - PSSB Suite 3500 - 95817 Sacramento CA
Identification of unique metabolite networks between Latino and Caucasian patients with nonalcoholic fatty liver disease (NAFLD) (part V)
STUDY_SUMMARY
Nonalcoholic fatty liver disease (NAFLD) is a spectrum of liver pathology ranging from simple steatosis to nonalcoholic steatohepatitis (NASH); the latter is characterized by inflammation and fibrosis. Risk factors for NALFD include obesity, diabetes, hyperlipidemia, and hypertension—all of which are features of metabolic syndrome. NAFLD is a very heterogeneous disease, as it presents in different patterns in males and females and in patients from different ethnicities, with unclear predictors for development and severity of disease. Previous studies have shown that NAFLD is 1.4 times more frequent in Hispanics than in Caucasians. One of the major challenges in NAFLD is the lack of accurate, noninvasive biomarkers for the detection of the most aggressive presentation, NASH. The gold standard for the diagnosis is liver biopsy, which is an invasive procedure associated with possible complications. Noninvasive diagnosis of NASH is a major unmet medical need and there are no ethnicity-specific biomarkers that can diagnose this condition and predict its progression. Therefore, the main gap in knowledge that this proposal and line of research will address is the characterizing the different plasma and liver metabolomics profile of patients with fatty liver from two ethnicities (Latinos vs. Caucasians) and of both sexes. The overall hypothesis of the present study is that the higher incidence of nonalcoholic fatty liver (NAFL) in Latino patients is reflected in a different plasma and liver metabolomics profile compared to Caucasian patients with further sex-related differences. Characterization of metabolite networks can aid in identifying the mechanistic underpinnings of sex and ethnic driven differences in NAFL which could help diagnose and establish a prognosis of this condition, especially in the critical transition from NAFL to the more aggressive nonalcoholic steatohepatitis (NASH).To address this hypothesis, plasma metabolomics profile of samples from male and female Latino and Caucasian bariatric surgery patients with NAFL and from healthy subjects will be compared. Metabolomics findings will be related with liver pathology and liver transcriptome profiles from intraoperatively obtained liver biopsies using correlation, network, and pathway analysis.
INSTITUTE
University of California, Davis
DEPARTMENT
Department of Internal Medicine, Division of Gastroenterology and Hepatology
LABORATORY
Medici Lab
LAST_NAME
Medici
FIRST_NAME
Valentina
ADDRESS
4150 V Street - PSSB Suite 3500 - 95817 Sacramento CA
Metabolic profiling of Rafflesia-infected Tetrastigma and applications for propagation
STUDY_SUMMARY
Endemic to the forests of Southeast Asia, Rafflesia (Rafflesiaceae) is a genus of holoparasitic plants producing the largest flowers in the world, yet completely dependent on its host, the tropical grape vine, Tetrastigma. Rafflesia species are threatened with extinction, making them an iconic symbol of plant conservation. Thus far, propagation has proved challenging, greatly decreasing efficacy of conservation efforts. This study compared the metabolites in the shoots of Rafflesia-infected and non-infected Tetrastigma loheri to examine how Rafflesia infection affects host metabolomics and elucidate the Rafflesia infection process. Results from LC-MS-based untargeted metabolomics analysis showed benzylisoquinoline alkaloids were significantly elevated in non-infected shoots and are here reported for the first time in the genus Tetrastigma, and in the grape family, Vitaceae. These metabolites have been implicated in plant defense mechanisms and may prevent a Rafflesia infection. In Rafflesia-infected shoots, oxygenated fatty acids, or oxylipins, and a flavonoid, previously shown involved in plant immune response, were abundant. This study provides a preliminary assessment of metabolites that differ between Rafflesia-infected and non-infected Tetrastigma hosts and may have applications in Rafflesia propagation to meet conservation goals.
The metabolomic resetting effect of FG4592 in AKI to CKD transition-day 21
STUDY_SUMMARY
C57BL/6 mice were anesthetized using isoflurane. UIR was induced by clamping the right renal pedicle for 45 minutes and then releasing it to allow reperfusion, leaving the left kidney intact. Sham treated mice served as controls. Each mouse was located supine on a thermostatic pad (37 °C) to maintain its body temperature throughout the whole process. After 3 days of recovery, the mice received a daily intraperitoneal (i.p.) injection of FG4592 (10 mg/kg) or vehicle for 18 consecutive days. After treatment, the mice were sacrificed. Non-target metabolomics analysis was carried out using the kidney tissues of mice sacrificed at day 21 after UIR.
The metabolomic resetting effect of FG4592 in AKI to CKD transition-day 21
STUDY_SUMMARY
C57BL/6 mice were anesthetized using isoflurane. UIR was induced by clamping the right renal pedicle for 45 minutes and then releasing it to allow reperfusion, leaving the left kidney intact. Sham treated mice served as controls. Each mouse was located supine on a thermostatic pad (37 °C) to maintain its body temperature throughout the whole process. After 3 days of recovery, the mice received a daily intraperitoneal (i.p.) injection of FG4592 (10 mg/kg) or vehicle for 7 consecutive days. After treatment, the mice were sacrificed.Non-target metabolomics analysis was carried out using the kidney tissues of mice sacrificed at day 10 after UIR.